The ribosomal DNA internal transcribed spacer 1 (ITS1) of three wild populations of Exopalaemon carinicauda was cloned and sequenced. The phylogenetic relationship among Palaemoninae was discussed using ITS1 from GenBank database. The results show that the length of the ITS1 ranged from 345 to 384 bp. The mean contents of GC were higher than AT;79 variation sites and 39 haplotypes were obtained in ITS1; Nucleotide diversity and average number of nucleotide diferences were calculated to analyze the gene sequence variation. Eight kinds of microsatellites were found in E. carinicauda. The type of (GA) _n was rich in ITS1. AMOVA analysis results show that the genetic differentiation of the three groups was weak or only moderately differentiated.The molecular phylogenetic tree was constructed with NJ method using software MEGA 4.0 to study several species of the Palaemoninae molecular phylogeny. According to the NJ tree, different individuals of the same species, different species of the same genera were grouped together, in consistence with the morphological taxonomy.