Twenty-five ocular P. aeruginosa isolates, 12 exoU+ (cytotoxic) and 13 were exoS+ (invasive), were analysed for their genotypic and phenotypic characteristics. Among the exoU isolates, four were multidrug resistant. ExoU+ isolates had a large pan genome (average 6553 genes) whereas exoS+ had a smaller pan genome (average 6401 genes). ExoU+isolates carried a median of 1403 (963-1894) whereas exoS+ strains have 1137 (909-4033) accessory genes. Out of a total of 32 acquired resistance genes, 29 were present in the exoU+ and 11 in the exoS+ strains. Five clones (ST233, ST491, ST316 and ST308) were present in the isolates. ST308 and ST316 clones were multi drug resistant and acquired most of the resistance genes. Among exoS strains, none of the clonal isolates were multidrug resistant. ExoU isolates were resistant to seven of the eight tested antibiotics, except polymyxin B. In conclusion, the two different type III secretion system genotypes of ocular P. aeruginosa were diverse and possessed distinct genotypic and phenotypic characteristics.