Chromosome identification is the first step in genomic research of a species, but it remains a challenge in scallops. In the present study, fluorescence in situ hybridization (FISH) mapping of 19 fosmid clones was attempted and used for chromosome identification in Zhikong scallop (Chlamys farreri Jones et Preston, 1904). Data showed that 10 clones were successfully mapped, including 7 without and 3 with C ( 0 ) t-1 DNA. Among them, 2 represented multiple signals and made no contribution to chromosome identification. Karyotypic analysis and cohybridization indicated that the remaining 8 clones realized the identification of 8 chromosomes. All 10 clones were sequenced at both ends, which could be developed as sequence-tagged sites and used for the unification of the cytological and genetic linkage maps. This study shows that fosmid clones can benefit chromosome identification and will undoubtedly be useful for cytogenetic research in Zhikong scallop.