Four distinct Franciscana Management Areas (FMAs) have been proposed based on several lines of evidence including genotype, phenotype, population response and distribution. To determine if differences in external morphology fit this division, a canonical variate analysis was carried out for males and/or females from FMAs I to IV using up to 14 characters. A total of 78 adult specimens were analysed. More than 90% of the differences between groups were summarized by three canonical variates. Females were larger than males in all areas. Females from FMA IV were of intermediate length between those from FMA I and FMA III and individuals from FMA II were smaller than those from all other areas. Position of dorsal fin and morphology of the anterior body region, differentiate individuals from FMA I and FMA III. Morphological differences found in this study give additional support for the proposed FMAs. Since habitat characteristics and franciscana feeding ecology vary regionally, it is possible that observed morphological differences are due to ecological divergence for niche occupation. The indication of a discontinuous distribution, consistency between genetic and morphological evidence, and a short time genetic divergence, might indicate that franciscanas inhabiting FMA I represent a distinct subspecies.