Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically investigated this relationship. In this study we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas. The full radiation of pupfishes includes generalist, durophagous, and lepidophagous pupfish species. We compare phenotypic variation and covariation (i.e., P matrix) between 1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, 2) San Salvador Island pupfish populations not containing the full radiation of fishes, and 3) San Salvador Island pupfish populations containing the full radiation in sympatry. Additionally, we explore whether phenotypic covariation varies between purebred and hybrid pupfish. We found that the P matrix of SSI generalist populations not found in sympatry with specialists exhibited higher levels of mean trait correlation, higher levels of constraints, and lower levels of flexibility compared to generalist populations on other Caribbean islands and sympatric populations of all three species found on SSI. We also documented significant differences between hybrid and purebred phenotypic covariation, where hybrids displayed lower correlations between traits and higher levels of flexibility, which may produce differential fitness in the wild. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.