Bovine tuberculosis (bTB) is a disease of cattle that presents risk to public health, causing severe economic losses to the livestock industry and difficulty in eradication because of its complex epidemiology. The aim of this study was to identify relationships between Mycobacterium bovis strains from cattle in the State of Jalisco, and those of other States of México. Molecular fingerprints of 337 M. bovis isolates from Jalisco, and 1152 from other States of México were included in the study. Isolates were obtained from tubercles between 1997 and 2015. Evolutionary relationship was determined throughout spoligoforest (www.emi.unsw.edu.au/spoltools/). From 337 isolates from Jalisco, 59 spoligotypes were obtained, ten of them included 48% of all isolates in the state. Five spoligotypes were common to beef and dairy cattle. The molecular analysis showed eight clusters in a philogenetic three: one with three subclusters of nine isolates each, all from dairy cattle; four with two isolates, including dairy and beef cattle. All spoligotypes from Jalisco have been reported in other states, four of the most frequent ones: SB0673, SB0971, SB0669 and SB0140, were the same as in other states. The most frequent spoligotypes of M. bovis found in Jalisco were also the most frequent ones in other parts of Mexico. However, there is no evidence to conclude that Jalisco is the source of infection to other states since no information on movement and destination of cattle could be documented.