In this study in order to identify, determine and compared the genetic diversity of sea cucumber Holothuria parvain both regions dayer port and bostaneh port, 16s rRNA gene sequencing was used. A total of 417 nucleotide locus were determined, after consideration of 16s rRNA gene sequences in the NCBI database were consistent with belonging to the species Holothuria parva samples was confirmed. In total was 4 haplotype identified in two areas that One haplotype was common in both areas. Haplotype diversity in the dayer port with haplotype 2 and bostaneh port with 3 haplotypes, respectively, 83% and 50% was estimated. Genetic differentiation (Fst) Negligible 000.0 and divergences rate (Dxy) 0.0048 and high gene flow (Nm = 1874) between the two regions were estimated. Based on the results of this study are probably samples of Bostaneh port and Dayer port than a similar population, That because high gene flow between the two regions do not have much different and There is also a common haplotype, suggesting Holothuria parva in the Persian Gulf Using a common ancestor of Holothuria parva in the region.