A morphological, cytological and genetic comparison of putative conspecific populations of Spirastrella sp. cf. mollis (Porifera: Demospongiae) from both sides of the Isthmus of Panama revealed a very high level of genetic differentiation together with morphological and cytological differences. The main differences were the distribution of the spirasters within the choanosome, the size and shape of spirasters 1, and the size and shape of inclusions within type I cells. Consequently these two populations clearly belong to different biological species. The Atlantic one, S. hartmani sp. nov. corresponds to what previous authors have called S. cunctatrix in the Caribbean. The finding of this new species raises to three the number of Spirastrella spp. known from the Caribbean Sea. The Pacific species is named here S. sabogae sp. nov. The levels of gene divergence found between S. hartmani and S. sabogae (Nei's genetic distance D=2.30) were as high as those found between different genera in other groups of invertebrates. Similarly exceptionally high values of gene divergence have been found between other congeneric sponge species and may be indicative either of a higher rate of molecular evolution or a very slow rate of morphological evolution in the Porifera compared to other metazoans.