A cross sectional study was conducted from December 2014 to May 2015 in Gambella town municipal abattoir and health centers to investigate the prevalence of bovine tuberculosis, isolation and molecular characterization of its causative agents, and to assess its public health implications in Gambella, Ethiopia. Postmortem examination, bacteriological culturing, RD deletion typing, and spoligotyping were used for investigation. The overall prevalence of bovine tuberculosis in cattle was 13.2% (66/500) on the basis of detailed postmortem examination. Statistical significant difference was observed in the prevalence of bovine tuberculosis among different body conditioned animals (χ2 = 39.105, P=0.000 and breeds (χ2 = 24.996, P=0.000). Molecular characterization of 11 mycobacterial isolates from human patients using RD9 deletion typing showed that all were M. tuberculosis, and further spoligotyping of the isolates revealed that SIT289, SIT134, SIT1634, SIT142 and one new strain (not found in the spoligotype databases). Of these M. tuberculosis strains identified, SIT 289 and SIT134 were found in cluster with 45.5% (5/11) cluster rate. Lineage of the human isolates indicated that 27.3% (3/11) were in Euro-American, and 9.1% (1/11) Indo-oceanic family in TB-insight database. Interestingly, one isolate from animal taken from mediastinal lymph node was confirmed to be M. tuberculosis using RD4 deletion typing and spoligotyping, in which the isolate was identified as SIT523 with Indo-oceanic lineage family. Awareness of cattle owners for bovine tuberculosis was found insufficient (22%), and the results also revealed the presence of potential risk factor for zoonotic transmission. In conclusion, isolation of M. tuberculosis in cattle, and occurrence of various strains of M. tuberculosis in the communities warrants further systematic investigation on the transmission of the disease in Gambella region of Ethiopia.