Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon. We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs. We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production.The Illumina BovineHD 777K BeadChip (genome build Bos taurus UMD3.1) in PLINK format (.ped and .map files) is included. A phenotype file (.csv) stating the breed, sex, age and M. bovis status of the cattle samples involved in the study is also included.  The files contain data on 228 Fulani and Mixed breed cattle from Cameroon and 216 reference cattle taken from Bovine HapMap Consortium (2009) and Bahbahani et al. (2017).