Anuran malformations are rarely reported to occur with high frequencies in natural populations. However, there is consensus that they can be caused by several factors. Herein, we report malformations in Rhinella ornata toads from land-bridge islands and compare their frequency with those of mainland populations from Rio de Janeiro. All islands showed levels of malformation significantly higher than the threshold of 5%, and one of the islands, Ilha Grande—which is the largest, farthest from the coast, and has been isolated for the longest time—had the highest frequency of morphological defects. Although it is possible that factors such as chemical contamination and parasite infection cause these defects, we also propose populational bottlenecks as contributing to the high frequency of malformations. Further studies are needed to understand the causes and consequences of malformations in these insular populations.