Interference with the host post-translational mechanisms, such as protein phosphorylation, is a key strategy used by many intracellular bacterial pathogens to subvert host immune cell function. Virulent non-tuberculous Mycobacteria (NTMs) unlike attenuated or non-pathogenic NTMs, successfully reside and multiply within the phagosomes of phagocytic cells such as monocytes and macrophages. Several studies have suggested that virulent NTMs alter host protein activation to enhance their survival. Macrophages play a very important role in the innate clearance of intracellular pathogens including NTMs. Low virulence NTMs such as Mycobacterium avium subsp. hominissuis 100 (MAH 100), and Mycobacterium abscessus subsp. abscessus are cleared from mice, whereas the highly virulent strains such as MAH 104 and MAH 101 disseminates and replicates in mice organs such as lungs, spleen, and liver. In this study we compared the macrophage early response to M. avium subsp. hominissuis (MAH) strains, M. abscessus, and a non-pathogenic Mycobacterium smegmatis. Our findings indicate that infection of the macrophage with MAH 100, M. abscessus, and M. smegmatis favors the development of M1 macrophage phenotype, while infection of the macrophage with MAH 104 inhibits M1 phenotype and favors the development of M2 macrophage, an anti-inflammatory phenotype associated with the healing process. By comparing protein phosphorylation patterns of infected macrophages, we observed that uptake of both MAH 100 and M. smegmatis resulted in MARCKS-related protein phosphorylation, which has been associated with macrophage activation. In contrast, in macrophages infected with MAH 104, methionine adenosyltransferase IIβ, an enzyme which catalyzes the biosynthesis of S-adenosylmethionine, was phosphorylated 15 min post-infection. S-adenosylmethionine is a methyl donor for DNA methylation. Inhibition of DNA methylation with 5-aza-2 deoxycytidine, significantly impaired the survival of MAH 104 in macrophages. Our findings suggest that the virulent MAH 104 enhance its survival in the macrophage possibly through interference with the epigenome responses (DNA methylation) while inhibiting the activation of MARCKS-related protein.