Enterococcus faecalis is an emerging nosocomial pathogen with a problematic and growing arsenal of antimicrobial resistance (AMR) determinants. While microbial surveillance strategies have been advancing in Western countries, data from other regions remain sparse. This study analyzed the genomes of nine South African E. faecalis isolates from four different provinces, collected between 1964 and 2015. In silico methods revealed limited AMR potential for the isolates sequenced here. However, the nine genomes were considerably diverse, as novel sequence types were identified. When compared to all publicly available E. faecalis genomes (n = 6,450 total genomes), the South African isolates sequenced here were most closely related to a mixture of clinical and environmental isolates from multiple countries. However, the limited number of public genomes, combined with sampling biases and the inherent diversity of E. faecalis, prevented precise determination of the origins of the South African isolates sequenced here. Instead, the relatively large genomic diversity suggests that these isolates are endemic to the region. Overall, this study underscores the importance of increased sampling and sequencing efforts in under-represented world regions, as genomic data from these regions will enhance our understanding of region-specific genetic traits and microbial dissemination, which could guide the development of preventive strategies.