Background <p>Cystic echinococcosis, a neglected parasitic cyclo-zoonosis is endemic in the Indian subcontinent. The etiological agent for this potentially fatal disease is a cryptic species complex, <i>Echinococcus granulosus</i> sensu lato (s. l.). The present study aimed at evaluating the role of small ruminants in circulating various <i>E. granulosus</i> s. l. genotypes in north India.</p> Methods and Results <p>The cladistics, haplotype network and genetic structure analyses were performed on the <i>E. granulosus</i> s. l. isolates collected from the slaughtered small ruminants (<i>n</i> = 1049) of north India (Chandigarh, Himachal Pradesh and Haryana) along with GenBank-archived <i>E. granulosus</i> s. l. sequences (<i>n</i> = 20) of ruminant origin from the Indian subcontinent by targeting the mitochondrial <i>nad5</i> gene. The NCBI BLASTn analysis revealed the presence of zoonotic genotypes G1, G3 (<i>E. granulosus</i> sensu stricto), G5 (<i>E. ortleppi</i>), and G6 (<i>E. canadensis</i>). Haplotype network analysis exhibited the presence of 14 haplotypes, where the haplotypes corresponding to <i>E. granulosus</i> sensu stricto (s. s.) species (genotypes G1 and G3) were arranged in a stellate conformation. High haplotype (0.837 ± 0.059, 0.836 ± 0.068 and 0.894 ± 0.078) and low nucleotide (0.0249 ± 0.0104, 0.0369 ± 0.0142 and 0.0036 ± 0.0008) diversities were recorded for the overall data set, as well as Indian and Pakistani <i>E. granulosus</i> s. l. populations, respectively.</p> Conclusion <p>Based on the mitochondrial <i>nad5</i> gene, the present study provided comprehensive insights into the cladistics and population structure of <i>E. granulosus</i> s. l. genotypes circulating in north India and highlighted the role of sheep/goat-dog cycle in the circulation of the zoonotic genotypes.</p>