Lineage 1 is an ancestral lineage of the Mycobacterium tuberculosis complex (MTBC) comprising five sublineages. In a previous study, we suggested that a representative of sublineage L1.1.3, present in both Mozambique and northern Brazil, SIT129, may have been brought to Brazil by sea during the long history of slavery that lasted, between Africa and Brazil, from the early 16th century to the mid-19th century. In this study, using a combination of new comparative genomics results and human migration data extracted from the SlaveVoyages.org database, we sought to more precisely reconstruct the scenario for the introduction of L1 genotypes into Brazil. We present results showing substantial similarities between the MTBC population structure in present-day Mozambique and Brazil across three subclades, L1.1.2, L1.1.3, and L1.2.2, and convergent historical data. Indeed, several introductions between the 16th and 19th centuries could explain the higher contemporary prevalence of L1 in northern Brazil. Our data do not allow us to decide between a direct introduction of L1 isolates into northern Brazil and intra-Brazilian transmission from the main southern ports, which seems likely. Other less likely scenarios are also discussed.