Tomato and chilli are economically important crops of Pakistan. Both of these are necessary part of our daily diet in the form of vegetables, salad and other culinary uses. Among biotic factors, the viruses are considered as substantial limiting factors reducing yield and deteriorating quality and quantity of tomato and chilli crops. The potyviruses like Chilli veinal mottle virus (ChiVMV), Potato virus Y (PVY), Pepper veinal mottle virus (PVMV), Pepper vein banding virus (PVBV) and Tobacco etch virus (TEV) have been reported as tremendous threats to the production of these crops worldwide including Pakistan. Management of plant viruses depends upon rapid and specific detection and identification, which is mostly facilitated by molecular techniques like PCR/RT-PCR/NA hybridization. The Molecular data on native Pakistani solanacious potyviruses was scare and their genetic variability was unknown. So the present research was conducted to determine the incidence, distribution and genetic variability based on molecular characterization of Pakistani solanaceous Potyviruses. A total of 2423 tomato and chilli leaf samples from 16 tomato and chilli growing districts viz; Badin, Thatta, Umerkot, Hyderabad, Tandu Allayar, Bahawalpur, Multan, Lodhran, Muzafargarh, Faisalabad, Vehari, Rawalpindi, Attock, Chakwal, Sialkot, Sheikupura, Karak and Loralai were collected in 2013-2014, of which only 920 samples were positive for potyviruses by PTA ELISA. Of these positive samples, the ChiVMV, PVY and ChiRSV were detected in 526, 323 and 71 samples respectively. The overall incidence of Potyvirus, ChiVMV, PVY and ChiRSV was recorded as 38%, 21.7%, 13.33% and 0.3% respectively. 20 The co-infections of ChiVMV and PVY was detected in 29 tomato samples and 31 chilli samples. While, co-infection of ChiVMV and ChiRSV and of ChiRSV and PVY in 18 and 24 chilli samples respectively. The highest incidence was recorded from Lodhran, Multan, Bahawalpur and Rawalpindi districts and the lowest from Karak, Loralai, Sheikhupura and Mansehra districts. The sequences of five ChiVMV, three PVY and 2 ChiRSV isolates were submitted to genbank. The Pakistani isolates of ChiVMV shared nucleotide identities of 90-97.5% with each other and 82.4-90.5% with other ChiVMV isolates. The nucleotide sequences of PVY isolates were 98.699.1% to each other and 98.2-99% with other PVY isolates. The ChiRSV isolates were 98.4% identical to each other, while they shared 92.6-98.1% identities with other ChiRSV isolates. The Pakistani isolates of ChiVMV clustered and shared maximum nucleotide identities with Indian isolates, while PVY and ChiRSV with chines isolates.