Eunapius is one of the most diverse genera in Spongillida with 17 species currently accepted. So far, only two records of this genus are known from Mexico: Eunapius fragilis from Xochimilco cited as Spongilla fragilis (by Rioja) and Spongilla fragilis var. zempoalensis from Zempoala lagoon (by Rioja). We revised Rioja’s original material, and new material from Zempoala lakes and considered that these records must be proposed as new species: Spongilla fragilis from Xochimilco is described as Eunapius xochimilca new sp., and Spongilla fragilis var. zempoalensis is described as E. zempoalensis new comb. In addition, we described two new species, E. gamundii and E. acanthostrongylae new spp. The main morphological characteristics that define these new species focus on the oxeas and gemmuloscleres morphology and size, as well as the shape and size of the gemmules. Their morphological differences are also supported by nuclear-ribosomal molecular markers, specifically the ITS region (ITS1-5.8S-ITS2), which were used to assess the phylogenetic relationships of the genus Eunapius. Tree topology showed genus Eunapius in a monophyletic clade composed of three main groups, which were clustered together with other genera of the family Spongillidae. Our results also support the previous molecular hypothesis, which suggests the polyphyly of Spongillidae and the need to reevaluate the taxonomy at the family level.