Genetic diversity of red-pigmented vibrios from different mangrove rhizospheres (Porteresia coarctata, Avicennia marina and Rhizophora mucronata) collected from Pichavaram mangrove, India was investigated. Twenty red–pink pigmented strains were isolated, 16S rRNA gene analyses indicted that these isolates belong to the genus Vibrio and were phylogenetically closely related to the type strains of Vibrio rhizosphaerae and Vibrio ruber. The rep-PCR analysis using GTG5 and BOX primers had similar groupings, and segregated these pigmented Vibrio isolates including two type strains into seven unique genotypic groups (REP groups A1–A7). The rhizosphere of P. coarctata harbors highly genetically diverse groups of red-pigmented vibrios compared to other plants. Multilocus sequence analysis using four genetic loci (pyrH, recA, rpoA, 16S rRNA) clearly supported the hypothesis that strains MSSRF38 (REP group A5) and MSSRF39 (REP group A6) could represent new Vibrio species. Biological functions of these vibrios were also determined and it was found that all these isolates have antagonistic activity against phytopathogens, and isolates belonging to REP groups A5 and A6 were positive for nifH gene by PCR. In conclusion, this study for the first time demonstrates the occurrence of genetically diverse groups of antagonistic, diazotrophic red-pigmented vibrios from different mangrove plants and suggests a new ecological role for vibrios as heterotrophic plant associated rhizobacteria.