Insular dwarfism is common in mammals. Many theories have been put forward to explain it, including competitive release, predation release, resource limitation and limited dispersal abilities. However, recent analyses have challenged many of these assertions and indicate that size evolution is more complex with populations and species developing unique patterns of morphological variation. We explore the evolution of body size in a poorly studied island carnivore, the pygmy raccoon Procyon pygmaeus, and compare it with other mainland and island populations within its genus. We studied 36 males and 42 females of the endemic and endangered pygmy raccoon on Cozumel Island, Mexico, from 2001 to 2003. Insular P. pygmaeus are, on average, 17.5% smaller in linear dimensions than their closest mainland relative. Minimum linear rate of size change was 6.21% per 1000 years or 5.43 darwins. Size reduction is likely to have been an adaptation to fewer resources and predators. Our population genetic examination identified different patterns of divergence than the morphological examination, indicating that the rate of morphological evolution likely exceeds that represented in this genus’ neutral genetic history. This case study highlights the importance of an autecological approach toward examining insular dwarfism given that clear patterns are not visible across the Carnivora.