Marine community datasets are key to the effective management and conservation of marine ecosystems, including coral reefs, which are increasingly threatened by a myriad of stressors. Although community information exists for many comparatively well-studied taxa, other common groups remain to be examined for even such basic information. In this study, we report on the zoantharian communities (Cnidaria: Anthozoa: Hexacorallia: Zoantharia) on the reefs of Bonaire in the southern Caribbean, and compare current results from 30, 20, 10, and 5 m depths to recent similar surveys from nearby Curaçao. The surveys revealed a total of 17 zoantharian species and epibiotic associations on the reefs of Bonaire. Additionally, results showed that while zoantharian assemblages around Bonaire at shallow 5 and 10 m depths, dominated by Palythoa spp., were similar to those found on Curaçao, diversity and numbers of zoantharians were higher at 20 and 30 m due to more abundant epibiotic Parazoanthidae species associated with sponges. Differences in assemblage structure were seen in deeper 20 and 30 m depths between the two islands, implying that conservation of deeper reef slopes, or along depth gradients, may need to be independently considered and addressed for each location. Analyses with environmental parameters on the Bonaire dataset indicate the potential importance of coral reef rugosity and physical structure in shaping these zoantharian communities, aspects that should be focused on in more detail in future research.