Lymphocyte antigen-6 (Ly-6) superfamily members have been identified in zebrafish, but the expression and function of these Ly-6 genes remain largely unknown. Posterior lateral line (pLL) system is produced by migrating pLL primordium (pLLp). Chemokine signaling, Notch, Wnt, and fibroblast growth factor (FGF) signaling regulate migration of pLLp cells and formation of neuromasts. However, the mechanism of neuromast deposition remains to be explored. Identification of novel genes expressed in pLLp will certainly help the study of such a process. Here we identified a Ly-6 gene called neuromast-expressed gpi-anchored lymphocyte antigen-6 (negaly6), which was specifically expressed in neuromast. Quantitative real-time PCR (qRT-PCR) analysis showed that negaly6 started to be expressed at 24 hpf, and whole-mount in situ hybridization analysis indicated that negaly6 was highly expressed in the trailing zone of pLLp and mature neuromast. Furthermore, negaly6 expression was inhibited by FGF signaling antagonist but not by Wnt signaling agonist or antagonist. Collectively, these data indicate that negaly6 may be associated with the regulation of neuromast deposition via FGF signaling pathway.