Coral reefs are one of the most diverse ecosystems found on earth, and are home to many habitat-specific fish. The Gobiidae family is known to be one of the most habitat-specific groups. Two common gobies found in the Caribbean are Coryphopterus lipernes and Gobiosoma evelynae, and both species rest on live coral heads. This study was conducted to determine if C. lipernes and G. evelynae show a preference for certain coral species and if the presence of disease affects this selection. A benthic survey was performed using video transects and CPC data analysis, allowing calculation of percent frequency for each coral species and frequency of diseased corals. Goby searches were conducted using SCUBA within a depth range of 10 - 15 m along the reef, recording the coral of choice and its disease status. The results showed that C. lipernes selected for 3 coral species and against 5, favoring Colpophyllia natans and Montastraea cavernosa. G. evelynae selected for 3 coral species and against 5, favoring M. cavernosa and Stephanocoenia spp. Both goby species selected significantly against coral disease, C. lipernes had a mean disease selection ratio of 0.39, and G. evelynae showed a complete selection against disease. Coral reefs are important ecosystems that are currently under significant abiotic and biotic stressors. It is important to understand the influence that an increase in disease and reduction in coral abundance may have on habitat-specific fish.