Different agroecosystems of southern Karnataka sampled for plant associated mites recorded six genera of tetranychid mites viz., Aponychus, Eutetranychus, Oligonychus, Petrobia, Schizotetranychus and Tetranychus. Neutrality test revealed a lowest haplotype diversity (0.993) of T. neocaledonicus population and Tajima’s D and Fu’s Fs test values were negatively significant for T. fijiensis, E. orientalis and S. baltazari populations, indicating the greater expansion of populations. Genetic analysis with ITS2 (rDNA) sequences revealed highest similarity between mite genera Petrobia and Aponychus showing lowest genetic distance of 0.51. Schizotetranychus has sister relationship with Eutetranychus which in turn clustered with Petrobia and Aponychus. Tetranychus and Oligonychus genera with lower genetic distance of 0.60 are clustered together. The study confirmed the clustering of morphologically related genera and lower genetic distances observed between related genera, expressed sister relationship. Molecular phylogenetic analysis of species under genus Oligonychus showed clustering in line with the morphology-based species taxonomic keys, while polyphagous species under the genus Tetranychus did not express form this grouping. Genetic diversity study of ten polyphagous mite species across their host plants and geographical occurrence revealed grouping according to locations in the phylogenetic tree. However, populations of Oligonychus tylus with a narrow host range showed close relationship for host plants than geographical locations which was evident in phylogenetic tree branching.