Pseudomonas aeruginosa is the commonest pathogens from ocular and lung infections. Various virulence factors contribute to its disease pathogenesis, particularly genes related to type III secretion systems. This study analysed strains of P. aeruginosa from ocular infections, from both Australia and India, as well as Australian strains from cystic fibrosis for the presence of various virulence genes. DNA from each strain was sequenced on Illumina® MiSeq bench top sequencer generating 300 bp paired-end reads. The sequences were assembled using Spades v3.12.0 and examined for the presence of virulence genes using the virulence factor database (VFDB, http://www.mgc.ac.cn/VFS/). Genes for phospholipase D (pldA), cytolytic phospholipase (exoU) (p=0.03) and the type III secretion system-associated gene (pscE) (p=0.01) were more common in Indian than Australian ocular isolates. A comparison between Australian isolates collected from different years (2004-2006 vs. 2017-2019) found that the recent isolates were more likely to possess alkaline protease aprA (p=0.02) and the type III secretion-associated toxin exoT (p=0.03). The comparison between recent and historical Indian eye isolates (1997-2006 vs. 2017-2018) found that the more recent isolates were more likely to possess genes for pilus synthesis (pilC), phenazine biosynthesis (phzD1) and exoU (0.01). In comparison to Australian cystic fibrosis isolates, more Australian eye isolates possessed genes for pyochelin receptor (fptA) (p=0.02), alkaline protease (aprA) (p=0.02) and type III secretion-associated toxin exoT (p=0.03) but less possessed the quorum sensing-associated gene ahII (p=0.02). In conclusion, these differences in possession of various genes between Australian and Indian eye isolates and Australian eye and lung isolates may be related to their pathogenicity.