The diversity of nitrogen fixing bacteria in any system must be identified to in order to fully understand their ecological role. PCR is commonly used to investigate bacterial diversity. To capture the full diversity PCR primers must bind to and amplify all targeted DNA sequences. For this study I analyzed published universal nifH primers' ability to capture the full diversity of nitrogen fixing bacteria. Based on this work I developed a new protocol for capturing the full diversity of nifH sequences. Using this optimized protocol I investigated community differences in nitrogen fixing bacteria between orange and brown color morphs of the Caribbean coral Montastraea cavernosa among three geographic locations. Whole community analysis revealed no difference between morphs or location. However, specific groups of proteobacteria and cyanobacteria differed in abundance between the morphs, indicating specific bacterial groups are responsible for differences previously observed in fixation between color morphs.