Abstract: This study determines conservation and functional divergence of Methylenetetrahydrofolate reductase (MTHFR) focusing on sites which bear single nucleotide polymorphisms (SNPs). We constructed its phylogeny and calculated type 1 divergence to identify regions of MTHFR under selection. We found that MTHFR is present throughout the three domains of life; Archaea, Bacteria and Eukarya. MTHFR well conserved preserving its function. It has been reported in earlier studies that polymorphisms in this gene are potential modulators of therapeutic response to anticancer drugs. Hence, SNPs in protein coding region were analyzed for the conservation and functional constraints. We report in this study that SNPs of MTHFR gene occur at sites under functional constraint i.e., these sites tend to be conserved. It is possible that SNPs at such sites could be fixed and propagated in a given population.