The production of quality silk in sericulture is the result of a combination of best managerial practices and the development of resistant breeds/hybrids, which is the primary strategy to control diseases in the current climate change scenario. Nearly all Bombyx mori silkworm breeds are vulnerable to viral flacherie caused by Bombyx mori bidensovirus (BmBDV), including the productive bivoltine breeds CSR2 and CSR27, which are widely bred by sericulture farmers in Southern India. However, in silkworm (Bombyx mori), resistance to the Indian isolate of BmBDV is governed by the recessive gene nsd-2 (non-susceptible to DNV-2) and can be utilized as a genetic marker to screen silkworm germplasm resources (SGR). To develop BmBDV-resistant silkworm breeds CSR2R and CSR27R, J2P (BBE-R) resistant to BmBDV was backcrossed for five generations with CSR2 and CSR27 parents, followed by sib-mating to identify individuals with the resistant genotype using marker-assisted selection. This was further validated through bioassay studies after feeding virus inoculum to the BmBDV-resistant progeny. The developed CSR2R and CSR27R breeds showed over 90% survivability to BmBDV infection, and their yield were at par with the to the existing control under laboratory conditions. The double hybrids developed using CSR2R and CSR27R as parents were tested at designated locations in southern India and showed a 3–8% improvement in survivability with an average yield increase of 3–5kgs per 100 DFLs compared to the control, with an exception at one test location, RSRS Anantapur, which showed an average of 17% increase in yield per 100 DFLs during autumn and spring seasons.