Fasciolosis in ruminants in India is caused by the liver fluke Fasciola gigantica. Radix (Lymnaea) spp. are known to carry the infective stages of this parasite. Understanding the seasonal prevalence of F. gigantica infection in the intermediate host is of extreme importance in order to elucidate the transmission dynamics of the parasite. So the present study was designed to determine the bioclimatic distribution of larval stages of F. gigantica in Radix spp. snails as well as to explore the genetic diversity of F. gigantica in three geographical regions (Deccan plateau, Western Ghats and coastal region) of Karnataka. The lymnaeid snails were sampled (n = 2077) for a period of one year (June 2015 to May 2016) at 24 sites. The snails were morphologically identified and the infection status was established through cercarial shedding and nested polymerase chain reaction (PCR) based technique targeting second internal transcribed spacers (ITS-2) of nuclear ribosomal DNA. The sensitivity of PCR (8.2%) for detection of F. gigantica infection within snail is significantly higher than cercarial shedding (4.3%) with an overall prevalence of 5.1%. The prevalence of infection was higher in winter than in the rainy and summer seasons (6.2% instead of 4.6% and 4.3% respectively). Deccan plateau (5.8%) showed a higher prevalence of infection compared to Western Ghats (5.2%) and Coastal region (3.6%). The sequencing ITS-2 region permitted the identification of the parasite as F. gigantica which is having high implication in studying the population genetic structure of the parasite in the country. In conclusion, overall results indicated that Radix spp. snails harboured F. gigantica developmental stages throughout the year and nested PCR was found to be sensitive and specific for detection of F. gigantica infection in snails compared to routine parasitological techniques.