Significant morphological differences were found between orange roughy, Hoplostethus atlanticus, caught in 1993 on the Puysegur Bank and those caught on the Lord Howe Rise, New Zealand. A total of 17 separate body measurements and counts were taken from each fish. Treating the sexes separately, significant differences were found between sites when linear relations between eight particular body measures and standard length were compared. The eight measures indicating differences in shape were head length, snout length, orbit diameter, maxilla width, premaxilla length, caudal peduncle, gill raker count, and anal fin count. Discriminant functions were used to compare sites and sexes, and these permitted a >90% success rate in distinguishing fish from the two sites. A discriminant function could not be found which successfully separated two separate tows made on the Puysegur Bank, indicating that phenotypic differences do not vary as much within a site as they do between sites. All analyses made suggested that fish from the two different areas had different body shapes. Morphological differences, such as those found in the current investigation, could only arise if the fish populations from the two areas were relatively discrete. There may be some movement of fish between areas, quite possibly enough to bring about relative genetic homogeneity, but clearly there is insufficient to prevent the two populations from differing phenotypically. These differences suggest that morphometric analysis may be a useful tool for distinguishing New Zealand orange roughy stocks.