Cilacap Regency located in southern part of Central Java has quite a long coastline spanning from southern Nusakambangan beach in the west up to  Jetis beach in the east border between Cilacap and Kebumen Regency.  Sandy beaches of Cilacap coastlines provide favorable habitats for various crustacean, including mole crabs. Careful examinations on so called Emerita emeritus samples from Cilacap showed slight morphological differences in their second periopod to those previously described characters in E. emeritus Boyko. It was assumed that our samples were cryptic species of E. emeritus complex rather than E. emeritus Boyko. A length of 560 bp fragments of the cytochrome oxidase-1 was successfully sequenced from Emerita emeritus morphotypes of Cilacap coast to reveal possible existence of cryptic or E.emeritus complex species.  Homology test resulted in 83–86% similarity to E. emeritus sequences available in GenBank (KR047035). Our samples also had high genetic distances (0.152–0.155) to the sequence of KR047035. The phylogenetic tree showed a clear separation between our samples and reference sequence (Emerita emeritus KR047035) with quite a long branch. The low genetic similarity, high genetic distance, and branching pattern of phylogenetic tree confirmed that our Emerita samples most likely did not belong to previously identified Emerita emeritus Boyko although showing slight morphological differences. These results indicated that possible cryptic species of Emerita emeritus or E. emeritus complex were lived in sandy beaches of Cilacap coastlines. It has been described that cryptic species are common in aquatic organisms. However, more samples are required to examine and confirm our finding.