A new lineage of Mycobacterium tuberculosis complex, named L10, has been identified in central Africa. Analysis of genome sequencing data from over 100,000 genomes using TB-Annotator software revealed this lineage, which is sister to M. africanum lineages L6 and L9. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum. The study used the TB-Annotator platform to analyze 102,001 M. tuberculosis complex isolates from the NCBI public domain. SNPs from 15,699 isolates were used to build a phylogenetic tree, identifying L10 as a lineage branching between L6 and L9 and the animal lineage A1. The two genomes representing L10 were obtained from strains isolated in the DRC and Belgium. These genomes lacked SNP markers from the latest M. tuberculosis complex lineage classification and no SNPs that confer drug resistance. Further analysis confirmed the phylogenetic position of the two genomes, showing they clustered between L6 and L9 and the animal lineage. The L10 lineage is characterized by a new region of deletion, IS6110 insertions, and 243 SNPs, including gyrA G7901T, recN C1920096T, and dnaG C2621730T. L10 is a sister clade to L6 and L9, revealing a putative previously missing piece in the evolutionary history and migrations of M. africanum. The study found that L10 strains are rare globally, likely restricted to central Africa. The genetic features of the strains, including their phylogenetic position, genetic distance from other lineages, distinctive regions of deletions and IS6110 insertions, and specific spoligotype signatures, led to the proposal of a new lineage. The findings extend the known diversity of M. africanum in Africa.A new lineage of Mycobacterium tuberculosis complex, named L10, has been identified in central Africa. Analysis of genome sequencing data from over 100,000 genomes using TB-Annotator software revealed this lineage, which is sister to M. africanum lineages L6 and L9. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum. The study used the TB-Annotator platform to analyze 102,001 M. tuberculosis complex isolates from the NCBI public domain. SNPs from 15,699 isolates were used to build a phylogenetic tree, identifying L10 as a lineage branching between L6 and L9 and the animal lineage A1. The two genomes representing L10 were obtained from strains isolated in the DRC and Belgium. These genomes lacked SNP markers from the latest M. tuberculosis complex lineage classification and no SNPs that confer drug resistance. Further analysis confirmed the phylogenetic position of the two genomes, showing they clustered between L6 and L9 and the animal lineage. The L10 lineage is characterized by a new region of deletion, IS6110 insertions, and 243 SNPs, including gyrA G7901T, recN C1920096T, and dnaG C2621730T. L10 is a sister clade to L6 and L9, revealing a putative previously missing piece in the evolutionary history and migrations of M. africanum. The study found that L10 strains are rare globally, likely restricted to central Africa. The genetic features of the strains, including their phylogenetic position, genetic distance from other lineages, distinctive regions of deletions and IS6110 insertions, and specific spoligotype signatures, led to the proposal of a new lineage. The findings extend the known diversity of M. africanum in Africa.