Despite being protected under the law, illegal trade in tortoises and freshwater turtles is common in India, with different species being trafficked for different markets. Indian species of tortoises and hard-shell turtles are predominantly trafficked for the pet trade and soft-shell turtles for the meat trade. Given their distinct markets, the operation of trade may vary between these different groups of tortoises and freshwater turtles, thereby necessitating different types of interventions. However, a systematic examination of illegal trade in tortoises and freshwater turtles that takes into account the differences between these markets is currently lacking. Here we compare the supply networks of tortoises/hard-shell turtles (in demand for pet trade) vs soft-shell turtles (meat trade), using information from 78 and 64 seizures, respectively, that were reported in the media during 2013–2019. We used social network analysis to compare the two networks and the role of individual nodes (defined as locations at the district or city scale) within these networks. We found that the tortoise/hard-shell turtle network had a larger geographical scale, with more international trafficking links, than the soft-shell turtle network. We recorded convoluted smuggling routes in tortoise/hard-shell turtle trafficking, whereas soft-shell turtle trafficking was uni-directional from source to destination. Within both networks, we found that a few nodes played disproportionately important roles as key exporting, importing or transit nodes. Our study provides insights into the similarities and differences in the illegal supply networks of different groups of tortoises and freshwater turtles, in demand for different markets. We highlight the need for intervention strategies tailored to address the illegal trade in each of these groups.