Cenotes are aquatic ecosystems with characteristic karst formations located throughout the Yucatan Peninsula, they represent Mexico’s hydrogeological heritage (Beddows et al. 2007). These systems originate from the dissolution of limestone and the subsequent collapse of underground cavities’ roofs. These cavities are fed by rainfall infiltration through calcareous soil structures, forming circular depressions connected to aquifers (Schmitter-Soto et al. 2002). The interaction between fresh and marine water generates chemical and biological stratification in these environments, as a result, cenotes constitute biodiversity reservoirs with high levels of endemism. These formations function as main connectors to the aquifer, housing highly specialized biological communities such as stygobiont crustaceans and fish adapted to low-luminosity and low-oxygen conditions (Camargo-Guerra et al. 2013; Álvarez et al. 2015; Angyal et al. 2021). This environment provides invaluable information about the dynamics of groundwater and the biogeochemical processes occurring in these ecosystems (Socki et al. 2002).

Recent studies of aquatic biodiversity in cenotes main focus is on crustacean taxa, including Copepoda, Remipedia, Ostracoda, Thermosbaenacea, Mysida, Amphipoda, Isopoda, and Decapoda (Suárez-Morales and Reid 2003; Boxshall et al. 2014; Álvarez et al. 2015; Angyal et al. 2018, 2020a, 2020b; Chávez-Solís et al. 2018; Espinasa et al. 2019; Chávez-Solís et al. 2020; Liévano-Beltrán and Simões 2021; Macario-González et al. 2021; Jaime et al. 2025), also fish from the families Cichlidae, Poeciliidae, Characidae, Pimelodidae, and Synbranchidae (Medina-González et al. 2001; Camargo-Guerra et al. 2013; Schmitter-Soto 2020), as well as gastropod mollusks (Grego et al. 2019) and photosynthetic microorganisms, particularly cyanobacteria and phytoplankton have been studied (Águila et al. 2022; Díaz-Hernández et al. 2023). However, for other taxa, such as sponges (Phylum Porifera), there has been a significant gap in research regarding the updating of their species richness, ecology and distribution in cenotes.

The first sponge species documented in cenotes from Yucatan were Spongilla lacustris (Linnaeus, 1759) and Ephydatia crateriformis, which is now recognized as Radiospongilla crateriformis (Potts, 1882), both were identified by Old (1936b). Penney and Racek (1968) later described a new species, Spongilla cenota, from a different cenote than those studied by Old (Table 2). Subsequent research by Poirrier (1976) confirmed that the material previously identified as S. lacustris in cenotes was actually S. cenota. Consequently, all specimens of S. lacustris found in Yucatan Peninsula cenotes were reassigned to S. cenota. Since these early studies, the biodiversity of freshwater sponges in Yucatan Peninsula cenotes has remained largely unexplored.

Mexico spans both the Nearctic and Neotropical regions, there, approximately 10 species of freshwater sponges (Spongillidae) have been documented across various aquatic ecosystems, including lakes, lagoons, and rivers in the country’s central and northern areas (Ehrenberg 1841; Potts 1885a, 1885b; Arndt 1933; Zorrilla 1935; Old 1936a; Martínez 1940; Rioja 1940a, 1940b, 1940c; Rioja and Herrera 1952; Rioja 1953; Bushnell 1971; Manconi and Pronzato 2005; Carballo et al. 2017, 2021; Gómez et al. 2019). In contrast, there are only two reports of marine sponges in cenotes from Quintana Roo, specifically those located near the coast with an influx of seawater, one from the genus Xestospongia (Suárez-Moo et al. 2024), and the marine endemic species Amphibleptula aaktun from the anchialine Aerolito cenote (Gómez et al. 2021). Notably, these marine sponges do not belong to the order Spongillida, which comprises predominantly freshwater species. Additionally, an unidentified sponge was recorded in Los Sabinos Cave in San Luis Potosí in the northern part of Mexico (Legendre et al. 2023). Overall, the knowledge of freshwater sponges in Mexican subterranean ecosystems is extremely limited compared to other freshwater habitats, where they have been studied more extensively.

The genus Ephydatia Lamouroux, 1816, is included among the freshwater sponges reported in Mexico. There are documented old records of E. fluviatilis (Linnaeus, 1759) and Ephydatia robusta (Potts, 1888) in lacustrine ecosystems, such as Lakes Xochimilco and Pátzcuaro in central Mexico (Potts 1885b; Zorrilla 1935; Old 1936a; Penney and Racek 1968). However, there are no recent status updates of this genus in Mexico. Ephydatia is a cosmopolitan genus widely distributed throughout the Northern Hemisphere and present in the Southern Hemisphere as well (Manconi and Pronzato 2008; Manconi and Pronzato 2016; Rasbold et al. 2023). These sponges primarily colonize rocky substrates and tree trunks in the shallow waters of ponds, rivers, lakes, lagoons and still bodies of water (lentic habitats) (Muricy et al. 2011; Nicacio and Pinheiro 2015; Evans and Montagnes 2019; Gost et al. 2023). There, they play important ecological roles in water filtration, food webs, and symbiotic interactions (Hall et al. 2021; Saxena 2021; Giudice and Rizzo 2024). Their extensive distribution and remarkable ability to thrive in diverse habitats make them particularly valuable for evolutionary and paleolimnological studies (Harrison 1988; Manconi and Pronzato 2016; Pisera et al. 2016). Considering the lack of updated information on Ephydatia in Mexican ecosystems, despite its ecological significance and scientific value, it is crucial to conduct new surveys to document its current distribution patterns.

This study documents the presence of Ephydatia fluviatilis in two cenotes in Yucatán, Mexico, using morphological by both Light Microscopy (LM) and Scanning Electron Microscopy (SEM) and molecular analyses to clarify its taxonomic identity and systematic position, including the investigation of diagnostic microcharacters. Our findings represent the first record of this species in subterranean freshwater ecosystems of the region and the first update for Mexico in over 80 years since its documentation in Lake Xochimilco (Rioja 1940a). This research expands current knowledge of sponge biodiversity in cenote environments, updates the known distribution of E. fluviatilis, and highlights its capacity to colonize diverse habitats. Furthermore, it provides a foundation for future studies on the ecology and biogeography of freshwater sponges in cenote ecosystems.

In Mexico, knowledge of the diversity and distribution of the freshwater sponge genus Ephydatia has remained outdated and underexplored. Old records report the species E. fluviatilis and E. robusta in Lake Xochimilco and Pátzcuaro (Zorrilla 1935; Old 1936a; Rioja 1942). Recently, the study by Rodríguez-Ríos et al. (2024) reported a sponge of the genus Ephydatia in Nazas River in Fernández Canyon, Lerdo, Durango; however, their study focused on insect larvae and the sponge species was not identified to species level. Therefore, our record of E. fluviatilis in cenote ecosystems extends the distribution range, updates the morphological description and integrates the first molecular data for this species in Mexico.

Earlier records are taxonomically problematic, Zorrilla (1935) and Old (1936a) merely mentioned the presence of E. robusta in Lake Xochimilco without providing formal descriptions, photographs, or illustrations to support identification. These authors variously identified specimens of the genus Ephydatia from this lake as Ephydatia subdivisa (Potts, 1888) (now recognized as a synonym of E. robusta), E. viridis (a taxonomically uncertain designation), and E. crateriformis (now reclassified as Radiospongilla crateriformis). Such inconsistencies underscore the considerable uncertainty that has historically characterized our knowledge of the genus Ephydatia in Mexico.

Recent taxonomic research examining freshwater sponge specimens collected during the last century has proven that historical identifications frequently require revision when subjected to contemporary molecular analysis and detailed morphological examination of spicules and gemmules. This need for taxonomic reassessment has been clearly demonstrated in studies of the genera Racekiela (Bass & Volkmer-Ribeiro, 1998) and Heteromeyenia in Mexico (Carballo et al. 2017, 2021). Consequently, a comprehensive review and update of the reported occurrences of Ephydatia species is essential to clarify the actual diversity and distribution of this genus in Mexico.

Despite the potential taxonomic ambiguity in Ephydatia species in Mexico, our study updates the biodiversity records of cenote sponges in Yucatan. Prior to this research, Ephydatia had not been documented in these ecosystems. With the inclusion of our records and the previously reported Spongilla cenota and Radiospongilla crateriformis (Old 1936b; Penney and Racek 1968), the number of known cenote sponge species has increased to three, each from a different genus. Additionally, two new cenotes were added to existing records, resulting in six cenote ecosystems with freshwater sponge populations (Table 2). Given the high number of cenotes in Yucatan (POETY 2021), further undiscovered species are likely.

Both previous and current studies consistently recorded sponges in open-type cenotes with vertical walls (Hall 1936; Beddows et al. 2007), suggesting that these environments may favor sponge presence. These cenotes receive sufficient light to support primary productivity and associated microalgae (Godefroy et al. 2019). Light exposure may also explain the observed color variation, as greenish-yellow coloration in illuminated specimens is likely linked to photosynthetic symbionts, a phenomenon reported in marine and freshwater sponges (Lemloh et al. 2009; Giudice and Rizzo 2024) and in other Ephydatia species (Hustus et al. 2023).

Future studies should aim to verify the records of S. cenota and R. crateriformis documented by Old (1936b) in their original locations. These include Xanaba Cenote Grande, Xanaba Cenote, and Dzadz Aguada, which are currently referenced only by their near location from the archaeological site Chichen Itzá (Table 2), rendering their precise geographical positioning is uncertain. Specifically, the Xanaba cenotes lack entries in the existing cenote database (POETY 2021), while multiple cenotes named Dzadz Aguada are located in different regions from Old’s (1936b) original description. This geographic ambiguity prevented us from accurately representing R. crateriformis locations on our cenote sponge map (Fig. 1). Instead, we provide an estimated reference point centered around Chichen Itzá, where these historical records might be situated.

Finally, this study emphasizes the importance of documenting and recording sponge populations in cenote ecosystems of Yucatan. With sponges frequently being overlooked in biodiversity inventories of cenotes, there has been a significant information gap for over 40 years regarding this taxonomic group (Cervantes-Martínez et al. 2018; Mejía-Ortiz and Yáñez 2024). As a result, numerous fundamental aspects of sponge ecology and biology within these ecosystems remain unknown, creating valuable opportunities for future research. These research opportunities include investigating the specific environmental conditions that determine sponge presence and absence in cenotes, as well as understanding their spatiotemporal distribution patterns throughout the cenotes network in Yucatan.

Research on freshwater sponges can provide important insights into water chemical conditions (Hill and Hill 2002), illustrate the evolutionary history of ecosystems (Erpenbeck et al. 2020), and offer valuable resources for biotechnological applications (Keller-Costa et al. 2014; Giudice and Rizzo 2024). Additionally, comprehensive sponge records will help complete the understanding of species diversity in cenotes, potentially supporting conservation efforts for these unique ecosystems. It is noteworthy that most of the cenotes where sponges have been reported are not located within the “Reserva Estatal Geohidrológica Anillo de Cenotes,” a Natural Protected Area (known in Spanish as ANP) established in 2013 (SDS 2013). Given this situation, it is imperative to intensify research efforts focused on understanding sponge populations together with their associated invertebrates, microalgae and microbiome in Yucatan’s cenote ecosystems.