Rifampicin resistance in Mycobacterium tuberculosis represents a big public health problem and the ponA1 gene could be related to this. Our study analyzed three secondary databases of 914 M. tuberculosis genomes, which were obtained from samples taken from patients of Lima and Callao cities. The following statistical tests were used to determine statistical association: Chi-square test, prevalence ratio (PR), and odds ratio (OR). We found that the presence of at least one SNP in the ponA1 gene was statistically associated with rifampicin resistance (ρ-values ​​of Chi-square test and OR < 0,05) and it was more likely to find an SNP of this gene in susceptible strains than in rifampicin-resistant strains (ρ-value of PR < 0,05). Likewise, two SNPs (P631S and A516T) were statistically associated with rifampicin resistance (ρ-values ​​of Chi-square test and OR < 0,05). A516T was more likely in resistant strains than susceptible stains, the opposite was found in P631S (ρ-value of PR < 0,05). In conclusion, the SNP A516T is statistically associated with rifampicin resistance and could generate phenotypic changes, which could alter rifampicin tolerance. © 2022, The Author(s) under exclusive licence to Archana Sharma Foundation of Calcutta.