Xanthomonas axonopodis pv. vignicola is the causative agent of bacterial blight, a destructive disease of cowpea in Africa. Laboratory studies were conducted with the objective of detecting variations among X. axonopodis pv. vignicola isolates which were collected from three different cowpea growing zones (Makurdi, Guma and Gboko Local Government Areas) in Benue state. The isolates were designated MKD388-1, GUM391 and GBK205-8 respectively. Isolates were cultured on Nutrient agar, tested for their Gram-staining reaction and their capability to utilize asparagine as a sole source of carbon and nitrogen. They were also subjected to biochemical tests. The genetic diversity of the isolates was assessed using Single Sequence Repeat (SSR) primers. Four primer combinations selected based on their reproducibility and amplification were used to differentiate the X. axonopodis pv. vignicola strains. Following these tests, the three isolates showed variations in color and growth character of colonies ranging from yellow to creamy colony color with mucoid growth. Variations to different biochemical tests were also observed among isolates. Primer assay showed genetic variation among the isolates as strains from Makurdi and Guma Local Governments showed high levels of molecular similarity while Gboko strain was distant. This study has lead to an understanding of the dynamics of pathogen variability that can be used to develop resistance gene pyramiding or gene deployment strategies. This will prevent selection for new virulence, which are effective against the currently available genetic sources of resistances genes.