Shigella sonnei is an important causative agent of bacillary dysentery worldwide that has recently emerged in developing countries. However, there are few studies that have characterized strains of S. sonnei isolated in Brazil. The aims of this study were to assess the presence of 12 virulence genes, the antimicrobial resistance profile against 16 drugs and the genotypic diversity of strains of S. sonnei isolated in this country. Seventy-two strains of S. sonnei isolated from human diarrhoeic faeces in São Paulo State, Brazil from 1983-2014 were studied. All of the strains contained the ipaH, iuc and sigA genes. The ipaBCD gene was detected in 19 % of the strains, the ial and virF genes in 18 % and the sen gene in 10 % of the strains. The set1A, set1B, pic,sepA and sat genes were not detected. A total of 42 (58.3 %) strains were resistant to trimethoprim-sulfamethoxazole. Thirty (41.6 %) strains were resistant to tetracycline. The S. sonnei strains were grouped in two clusters called A and B by PFGE and ERIC-PCR, and the majority of the strains comprised in each cluster presented ≥80 % similarity. In conclusion, the pathogenic potential of the strains studied was highlighted by the presence of important virulence genes. The high rates of resistance to trimethoprim-sulfamethoxazole and tetracycline are alarming once those drugs can be used in the treatment of shigellosis. The PFGE and ERIC-PCR results suggest that there are two prevalent subtypes in the studied strains of S. sonnei that differed little over 31 years and have been contaminating humans and causing diseases in São Paulo State, Brazil.