The simple sequence repeats (SSRs) are small 1-6bp tandem repeat elements present across diverse genomes and involved in gene regulation and evolution. Presently we analyzed SSRs in genomes of 98 species of family Polyomaviridae across four genera. The genome size ranged from 3962bp (BM87) to 7369bp (BM85) but maximum genomes were in the range of 5 to 5.5 kb. The GC% had an average of 42% and ranged between 34.69 (BM95) to 52.35 (BM81). A total of 3036 SSRs and 223 cSSRs were extracted using IMEx with incident frequency from 18 to 56 and 0 to 7 respectively. The most prevalent mono-nucleotide repeat motif was “T” (48.95%) followed by “A” (33.48%). “AT/TA” was the most prevalent dinucleotide motif closely followed by “CT/TC”. The distribution was expectedly more in coding region with 77.6% SSRs of which nearly half were in Large T Antigen (LTA) gene. Notably, most viruses with humans, apes and related species as host exhibited exclusivity of mono-nucleotide repeats in AT region, a proposed predictive marker for determination of humans as host in virus in course of its evolution. Each genome has a unique SSR signature which is pivotal for viral evolution particularly in terms of host divergence.