As a nutritious mollusk living in the intertidal zone, Onchidiidae has a significant value for biological research. Nine populations were collected from the costal areas such as Chongming (Shanghai), Ningde (Fujian), Haikou (Hainan) in this study. Through the study of anatomy and other methods to investigate the major category characteristics, the nine populations were preliminary classified. By sequencing segments of 18S rRNA gene and constructing phylogenetic trees using these nine populations and four other 18S rRNA gene sequences from GenBank, with Siphonaria as an outgroup, we analyzed the phylogeny of Onchidiidae in mainland China. The trees were used for discussing the relationship between the populations of the Onchidiidae in this study. The results showed that the southern coast has more populations than the northern coast in China. Besides two known species, Onchidium struma (JZH) and O. verruculatum (FJZ & HNZ), five new recorded species may exist: Onchidium(1), Platevindex(2), one Peronia(1) and Paraoncidium(1). The phylogenetic trees indicated that the nine populations can be divided into four subgroups, Peronia, Onchidium, Platevindex and Paraoncidium, and Peronia has the highest confidence level in clustering. Onchidium verruculatum (FJZ & HNZ) should be Peronia verruculata.