Variations in the population of lancelets inhabiting Chabahar Bay were surveyed statistically. Multivariate analysis of the Iranian Branchiostoma population using 5 morphometric characteristics indicates no separation of populations by locality in the study area (ANOSIM global; R = 0.2). Principal component analysis of the mean values of the 5 meristic characteristics of the present population with those of conspecifics of other populations around the world showed that Iranian lancelet populations are very similar to B. lanceolatum and completely different from the B. arabia and B. belcheri previously reported in adjacent waters (ANOSIM for pairwise tests; R = 1). Cluster analysis indicates that the Iranian B. lanceolatum shows greater affinity with its conspecifics in the Mediterranean than in the Indian Ocean. The distribution of lancelet populations correlates more closely with sand particles; however, this correlation was not significant (P = 0.28). The novel aspect of this study is the information presented about B. lanceolatum populations in the Iranian Gulf of Oman and its greater affinity with the species reported with Mediterranean conspecifics.