Species descriptions of most alcyonacean octocorals rely heavily on the morphology of sclerites, the calcium carbonate spicules embedded in the soft tissue. Sclerites provide taxonomic characters for species delineation but require qualitative descriptions, which introduce ambiguities in recognizing morphological features. Elliptical Fourier analysis of the outline of sclerites was used to quantify the morphology of eight species of gorgoniid octocoral in the genus Pseudopterogorgia. Sclerites from one to seven colonies of each species were compared. Scaphoids and spindles were examined separately; rods and octoradiates were excluded from the analyses because of their morphologic similarity across all species. Discriminant analysis of elliptical Fourier descriptors (EFDs) was used to determine whether the elliptical Fourier analysis could be used to identify the specimens. Sclerites were highly variable even within a single colony. Correct species assignments of individual sclerites were greater than 50% for both scaphoids and spindles. Species assignments based on averages of the EFDs for each colony approached 90%. Elliptical Fourier analysis quantifies morphological differences between species and measures colony variance in sclerite size and shape among colonies and species. Phylogenetic analysis based on EFDs did not capture monophyletic groups. The quantification of complex shapes such as sclerites provides an important tool in alpha taxonomy but may be less useful in phylogenetic analyses.