Abstract Genomic GC (overall G + C content of the coding sequences) variations were reinvestigated between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae species. It was observed that overall genomic GC variation between the species mainly originates from the combined effects GC 1 and GC 2 variations. But codons having identical amino acids with different codons (IA) (between the orthologous codon pairs) are responsible for the genomic GC 3 variation between the organisms, whereas orthologous codons having different amino acids (DA) between the two organisms are responsible for the variation of GC 1 levels. Further analyses indicate that duets and quartets are going in the same direction with same magnitude in changing the GC 3 levels for IA category, whereas GC 1 levels of duets of DA category decreases significantly from the overall GC 1 levels but GC 1 levels of quartets increases significantly from the overall GC 1 levels. GC 3 levels of informational genes for the IA category decrease more rapidly than the other functional categories of genes. The biological implications of these results have been discussed in this paper.