Recent research demonstrates important shifts in the skin microbiome with age, which may be linked to skin ageing processes. Nevertheless, very few studies have provided strain-level characterisation of the ageing skin microbiome, and functional assessment of host-microbe interactions remains limited. This work applies Oxford Nanopore sequencing for metagenomic profiling and for whole genome characterisation of bacterial isolates to evaluate their role in ageing. High-resolution profiling of young (<35 y, n=20) and old (>60 y, n=22) adults revealed that body site (forehead, arm, and foot) was the primary driver of bacterial community structure, with age as a secondary factor. Age-related changes included increased alpha diversity, distinct beta diversity, reduced Cutibacterium and Staphylococcus abundance, and enrichment of opportunistic taxa. Given the observed reduction in Staphylococcus abundance with age, we next assessed intraspecies diversity of S. epidermidis, a keystone skin commensal, to investigate potential age-associated phenotypes. Pangenome analysis revealed phylogenetic diversity among S. epidermidis strains within individuals. Interestingly, age did not significantly influence cluster distribution. Gene presence/absence patterns related to antimicrobial resistance, extracellular matrix degradation, and biofilm production were heterogeneous among strains and showed no correlation with volunteer age. These findings underscore the importance of exploring microbial diversity beyond species level and the need to identify factors driving such diversity, including the interplay between host genetics and the skin microbiome. Together, our work provides a foundation for understanding how bacterial strains contribute to skin ecosystem dynamics across the lifespan, paving the way for developing microbiome-based interventions to support skin ageing.