Breadfruit is a traditional, long-lived, staple tree crop that was domesticated in Oceania. Beginning in the late sixteenth century efforts were initiated to introduce breadfruit to other tropical regions. Today it is grown throughout the tropics, and the Caribbean is the second most important producer of breadfruit outside of Oceania. Despite its vast potential to increase food security, health, and income generation in tropical regions, breadfruit is an underutilized crop. A broad range of basic and applied research approaches will be critical to allow breadfruit to reach its potential. Plant genetic resources are the basis for food security, and the diversity they encompass will be the fodder for adaption to climate change and other stresses. Characterizing and conserving breadfruit genetic resources, including its wild relatives, will be at the core of the crop’s success. This study uses nuclear and chloroplast microsatellite markers to examine 423 individuals of breadfruit from throughout Oceania, the Caribbean, India, and the Seychelles as well as wild relatives. The aim of this study is to compare levels of genetic diversity throughout the islands of breadfruit’s native Oceania and beyond, assess the level of genetic diversity in breadfruit compared to its wild relatives and to other perennial crops, and assess the utility of microsatellite markers to differentiate among breadfruit cultivars. Findings suggest that there is a range in the levels of breadfruit genetic diversity across regions, with Melanesian breadfruit being among the most diverse. However, breadfruit from the Caribbean and other areas outside of Oceania demonstrate greater diversity than might be expected. Future efforts should focus on broadening the representation of breadfruit diversity (including its wild relatives) in research studies and in germplasm repositories, with samples from the Caribbean and Melanesian islands being important targets for further collection, conservation, and study.