Abstract: A new methodology was developed for etection and determination of the molecular variation of the potato spindle tuber viroid found in Fujian.A pair of primers was designed and synthesized based on the STVd gene isolated and amplified from the extracted viral RNA with RT-PCR.The specific fragment of 359 bp was isolated from the infected plants,but none from the healthy tissue samples.The fragment was amplified and subjected to validation by agarose gel electrophoresis.Then,the purified PCR product was cloned,sequenced and Blast searched to be identified as PSTVd isolate KM588065.1.The isolate shared 98% homogeneity with that from NCBI data bank.Comparing the sequence alignments of 3 other strains,the isolate appeared to contain 11 nucleotide polymorphisms with 5in the pathogenicity region.Based on the phylogenetic tree analysis on the DNA sequences of PSTVd from different countries and regions,this virus isolate was determined to be closely related to those from northern China,Europe and America,and only remotely related to that from New Zealand.