Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the 16S rRNA gene limits its use for studies of host-microbe co-evolution. In contrast, thecpn60gene is a universal phylogenetic marker with greater sequence variation capable of species-level resolution. This research compared mammalian skin microbial profiles generated fromcpn60and 16S rRNA gene sequencing approaches, testing for patterns of phylosymbiosis that suggest co-evolutionary host-microbe associations. An ~560 bp fragment of thecpn60gene was amplified with universal primers and subjected to high-throughput sequencing. Taxonomic classification ofcpn60sequences was completed using a naïve-Bayesian QIIME2 classifier created for this project, trained with an NCBI-supplemented curatedcpn60database (cpnDB_nr). Thecpn60dataset was then compared to published 16S rRNA gene amplicon data. Beta diversity comparisons of microbial community profiles generated withcpn60and 16S rRNA gene amplicons were not significantly different, based on Procrustes analysis of Bray-Curtis and UniFrac distances. Despite similar relationships among skin microbial profiles, improved phylogenetic resolution provided by thecpn60gene sequencing permitted observations of phylosymbiosis between microbial community profiles and their mammalian hosts that were not previously observed with 16S rRNA gene profiles. Subsequent investigation ofStaphylococcaceaetaxa using thecpn60gene showed increased phylogenetic resolution compared the 16S rRNA gene profiles, revealing potential co-evolutionary host-microbe associations. Overall, our results demonstrate that 16S rRNA andcpn60marker genes generate comparable microbial community composition patterns whilecpn60better facilitates analyses, such as phylosymbiosis, that require increased phylogenetic resolution.