|Potato (Solanum tuberosum L) is growing as a leading staple crop in Pakistan and ranked as fourth in economic significance of the world. It gives 12-15 times more yield per hectare as compared with cereals and calories production per unit area is higher then cereals. Among vegetable affecting virus, Potato virus Y (PVY) is one of the top five viruses and enjoys a promising position among the pathological constrains in the potato crop. It is getting alarming position with significant losses in Pakistan. The percentage incidence increased 4 % in Sahiwal, 7 % in Islamabad, 36 % in Rawalpindi and 67 % in Faisalabad as compare to the year 2010-11 and 2011-12. The over all mean percentage incidence was observed 22 % (2010-11) and 51 % (2011-12) which showed an increase of 29 % in second year. Higher percentage incidence of PVY seems to indicate the high aphid vector efficiency to transmit PVY in non-persistent manner, environmental parameters and the degree of resistance of potato varieties against PVY are also important factor in the spread of PVY disease. The virus is mechanically transmissible. A set of 5 healthy plants each, with 3 replications was inoculated with infected sap of PVY. Local lesions on Chenopodium quinoa, mottling on Nicotiana rustica, and necrotic whitish lesion symptoms on Nicotiana tabacum cv. Samsun were observed. Infection of Potato Virus Y in potato plants were confirmed to DAS-ELISA and amplification of 801 bp of coat protein gene of PVY by using gene specific primer through PCR. The cloned coat protein gene was sequenced for phylogenetic analysis of PVY isolates. The full length nucleotide sequencing of coat protein gene of 11 isolate revealed that the 3 different clusters. Pakistani isolates SPVY-CP-PK and FPVY-CP-PK falls in third cluster with two Chinese isolates. FPVY-CP-PK showed maximum similarities 99.992 %, 99.991 % and 99.984 % with China-H, SPVY-CP-PK of Pakistani isolates and China-AB3 respectively. SPVY-CP-PK was maximum similar with China-AB3 99.986 %, FPVY-CP-PK 99.984 % and China-H 99.82 %. China-AB3 and China-H were 99.984 % similar with each other. The finding of this study is that FPVY-CP-PK and SPVY-CP-PK have maximum genetic similarities with each other and other isolates of China. This similarity is due to the same group and both share maximum nucleotide homology. The other reason for low genetic diversity between Pakistani and Chinese isolates due to high conserve sequence of coat protein gene in genome of PVY. This work led to useful conclusion that there is very low genetic diversity in isolates of PVY which can be successfully utilized in epidemiological studies of PVY isolates in Pakistan. Further analysis of variation level in Pakistani isolates will help scientists to formulate appropriate PVY disease management strategies like coat protein gene mediated resistance. There is an ample scope of more detailed study by comparing more number of isolates with FPVY-CP-PK and SPVY-CP-PK.