The objective of this study was to determine the molecular pattern of M. bovis isolates from cattle of Northern Mexico and its relationship with some risk factors. Isolates (n=60) were obtained from the states of Coahuila (COA, n=14), Tamaulipas (TAM, n=16), Nuevo Leon (NL, n=14) and Baja California and Durango (DUR, n=16). The risk factors studied were: system of production (Dairy and Beef), state, age, lesion type (localized and generalized), and type of presentation (caseous and calcified). Samples were analyzed at the Regional Laboratory of Monterrey NL, following a spoligotyping protocol. Twenty-five spoligotypes belonging to the M. bovis complex were identified. Eleven (18.3%) isolates presented a unique pattern, whereas 49 (81.7%) were grouped in 14 clusters. The largest clusters had 12 and 17 isolates. The average heterozygocities per state were 21.4% (NL), 15.6% (TAM), 15.6% COA) and 9.9% (DUR). The genetic distances of the isolates between states did not show differences (P > 0.05) when examined by Chi-square tests. The average genetic diversity (15.6%) was due to the variation of strains within subpopulations. In this study an 8.3% difference among states was obtained, which suggest the idea of a unique strain of M. bovis with many variants and that the genetic diversity found for M. bovis could be in part due to the movement of animals between regions. Statistical analysis did not show association (P > 0.05) between risk factors and strains of M. bovis.