Abstract: The seali gene belongs to the PIWI superfamily and plays an important role in germ cell development. In this study, a unigene annotated as seali was screened from the gonad transcriptome database of Mesocentrotus nudus and named Mnseali. Subsequently, the full-length Mnseali cDNA sequence was obtained by 5′ and 3′RACE (rapid amplification of cDNA ends). The full-length cDNA of Mnseali was 3462 bp, containing an 84 bp 5′UTR, a 447 bp 3′UTR and a 2862 bp open reading frame (ORF), which encodes a protein of 954 amino acids. The polyadenylation signal of the 3′UTR was not the classic “AAUAAA” or “AUUAAA” sequence but “AAUACA”. Similar to that of other species, Mnseali also had highly conserved PIWI and PAZ domains and belonged to the PIWI subfamily of the Argonaute family based on the results of domain and phylogenetic analyses. Real-time quantitative PCR (RT-qPCR) analysis revealed that Mnseali was expressed in the gonad, intestine, tubular foot and coelomic fluid, with the highest expression level in gonads. In addition, Mnseali is a maternal factor and can be detected throughout embryogenesis. The Mnseali level significantly increased along with oogenesis. However, there was no significant difference in expression in the testis before maturation, and expression peaked at Stage IV. Moreover, in situ hybridization (SISH) of tissue sections showed that Mnseali was specifically expressed in the germ cells. The current study identified a germ cell marker to further study the mechanism of germ cell development in sea urchin.