Poikilothermic organisms are predicted to show reduced body sizes as they experience warming environments under a changing global climate. Such a shrinking of size is expected under scenarios where rising temperatures increase cellular reaction rates and basal metabolic energy demands, therein requiring limited energy to be shifted from growth. Here, we provide evidence that the ecological changes associated with warming may not only lead to shrinking body size, but also trigger shifts in morphology. We documented 33.4% and 39.0% declines in body mass and 7.2% and 7.6% reductions in length for males and females, respectively, in a wild population of Amargosa pupfish, Cyprinodon nevadensis amargosae, following an abrupt anthropogenically driven temperature increase. That reduction in size was accompanied by the partial or complete loss of paired pelvic fins in ~34% of the population, a morphological change concomitant with altered body dimensions including head size and body depth. These observations confirm that increasing temperatures can reduce body size under some ecological scenarios, and highlight how human-induced environmental warming may also trigger morphological changes with potential relevance for fitness.