The aim of this study was to investigate the genomic profiles of Nocardia. Three clinical Nocardia isolates were collected and conducted whole genome sequencing. Subsequently, 489 publicly available assemblies of Nocardia isolates were downloaded from the National Center for Biotechnology Information (NCBI) public database and identified genetic diversity. Three clinical isolates and 142 isolates from NCBI public database with 90 % evolution similar to our isolates were further analysis. Comparative genomics analysis clearly classified 145 isolates into two distinct evolutionary lineages. Average Nucleotide Identity (ANI) revealed 2 different species (N. cyriacigeorgica, N. farcinica) belong to 3 different clusters for three isolates. Antimicrobial resistance genes of rox and far-1 were only identified in N. farcinica, while ast-1 were found in N. cyriacigeorgica. All isolates carried virulent factors such as ahpC, icl, and mbtH genes, while virulent gene relA was only found in several N. farcinica isolates. Therefore, the present study provides insights into the genetic diversity of N. cyriacigeorgica and N. farcinica.