We documented the type two polyketide synthases(PKS II) gene diversity and novelty by sequencing KSα genes known to synthesize bioactive small molecules. Sequences were derived from culturable bacteria isolated from bats in Arizona and New Mexico. We targeted the PKS II pathway which comprised a large proportion of the culture collection. Genomic analyses of a 16-member subset of bat bacterial isolates were additionally explored to document total BGC diversity and novelty of the bat microbiome. Data used for PKS II gene variant number per isolate by state were comprised of number of amino acid sequences per isolate (Num_seqs_per_isolate) by state, with related isolate identification (Isolate ID) and isolate number (ID #). Data used for PKS II gene variant number per isolate by species were comprised of number of amino acid sequences per isolate (Num_seqs_per_isolate) and species, with related isolate identification number. In our effort to determine novelty of PKS II sequences, we compared experimental PKS II sequences to known and curated references sequences. In an effort to determine novelty of PKS II sequences to its taxonomic assignment, in general, we compared PKS II sequences to themselves. Data were used to create percent of bacterial isolates from bat skin with KSα detected by location and bat species. Data were also used to describe the bat microflora from which KSα sequences were isolated. Data in the form of genomic assembly statistics and biosynthetic capacity analysis of 16 Actinobacteria isolates from bats were used. Data were used to indicate the presence or absence of the KSα gene in isolates. All of these data were regarded as supplemental.