Line transect based abundance estimation is complicated for long-finned (LFPW, Globicephala melas) and short-finned (SFPW, G. macrorhynchus) pilot whales because of their similarity in appearance and their overlapping summertime range in some areas. We developed a photograph-based approach to distinguish between species of free-ranging pilot whales in the northwest Atlantic. We collected skin samples and photographs during the summers of 2004–2007 and used skin samples to distinguish species based on mitochondrial DNA. Relative morphometric measurements from photographs were examined using mixed-effect models and logistic regression. The best model among 94 candidate models had an overall classification error rate of 2.5%. We tested the presence/absence of pigmentation in four regions of the dorsal body (melon, eye, cape, and saddle) for differences. Pigmentation was present in all four regions in 100% of the SFPWs sampled. Melon patch, blaze, and saddle patch pigmentation were present in 6%, 68%, and 50%, respectively, of the LFPWs, but the cape was completely absent. Both types of analyses provided positive species discrimination of free-ranging animals. We created a cost-effective, simple tool which could ultimately assist in providing appropriate management, mitigation, and conservation strategies for both northwest Atlantic species of pilot whales.