In the present paper, 3325 and 563 EST-SSRs of two sea animal Paracentrotus.lividus and Aplysia. californica was in silico predicted by searching unigene databases, and the SSR length, frequency of different repeat types and compound SSR comprising was analyzed in detailed. The results showed that the SSR abundance of Aplysia unigene was more abundant then that of Paracentrotus . Tri- and dinucleotide motif was the most common motif in Aplysia and Paracentrotus SSRs, respectively. The SSR sizes, compound SSR comprising and motif frequency distribution was significantly different between these two sets of SSRs. The potential cross-species of selected SSRs was evaluated, demonstrating conserved di- or trinucleotide SSRs motifs and polymorphisms in length and nucleotides deleting and replacing exiting between these two species. Taken tighter, the results showed the unigene of Aplysia and Paracentrotus was enrich for developing of cross-species SSR markers and would facilitate evolution and comparative genome research of these two species.