Abstract Helicobacter pylori is predominantly transmitted within families and infection occurs mostly in early childhood, frequently leading to persistent infection lifelong. In the present study, genetic diversity of Helicobacter pylori among North and South Indian isolates was evaluated. 16S rDNA, cagA, vacA and iceA genes were amplified followed by sequencing of respective amplicons for diversity analysis. Result of PCR assay showed that status of pathogenicity genes varied among strains from Varanasi and Hyderabad. Phylogenetic analysis based on 16S rDNA sequences showed clustering of Hyderabad and Varanasi strains in separate groups, pointing to significant diversity. Additionally, phylogenetic analysis revealed that most of the Varanasi strains shared homology with the strains from Taiwan except for two isolates which matched with an isolate from Brazil. On the other hand majority of the Hyderabad strains showed relatedness with strains from Brazil except one which showed homology with one strain from Taiwan. In conclusion our results show that genetic diversity among H. pylori isolates is widely prevalent regardless of the region from which they are isolated. More interestingly, phylogenetic analysis suggests that the Indian strains of H. pylori show close homology to those from Taiwan and/or Brazil.