Coral reefs are becoming overgrown by fleshy and filamentous algae caused by a variety of local and global stressors. Coral reefs with higher percent coverage of fleshy and turf algae are enriched with bacterial members of the Bacteroidetes Phylum (formerly the Cytophaga-Flavobacterium-Bacteroides, CFB group). Members of the Class Flavobacteriia can be enhanced experimentally when reef-associated microbial communities were cultured with turf algal photosynthate. Previous studies have characterized temperate Flavobacteriia, but not those inhabiting tropical systems. This study isolated and analyzed the genomes of twelve Flavobacteriia and one Cytophaga strain harvested from in situ turf assemblages and turf algal-enrichment cultures. Genomic annotations of the thirteen tropical isolates were compared with those from four previously-described temperate Flavobacteriia. Protein- coding genes compared between these strains formed three distinct clusters. The first cluster contained two tropical members from the genus Salinimicrobium and two temperate strains Gramella forsetti strain KT0803 and Leeuwenhoekiella blandensis MED217. The second cluster contained two tropical members from the genus Aquimarina. The third cluster contained five members of the genus Tenacibaculum, one from the genus Winogradskyella and two temperate members, Dokdonia sp. MED134, Polaribacter sp. MED152. Finally, an outgroup formed with the isolate from the genus Cytophaga. Within two of the three clusters tropical and temperate members demonstrated distinct adaptations between environments. Reef metagenomes collected in situ from the central Pacific Line Islands were compared to assess the prevalence of these Flavobacterial genomes in reef environments with contrasting anthropogenic influences and benthic communities. Relative abundances of these Flavobacteriial isolates were higher in degraded reefs with high benthic coverages of algae, consistent with previous findings. In conclusion, coral-reef associated Flavobacteriia that are more abundant in degraded reefs form three clusters with features that distinguish them from previously-described temperate Flavobacteriia.