The paper presents molecular characterization data of quarantine fungus Diaporthe/Phomopsis vaccinii and related isolates. In 2002 this fungus was for the first time observed in Lithuania on Vaccinium corymbosum, later on V. macrocarpon. The identification of this pathogen is often difficult and lengthy when using only classical methods based on morphological features. Therefore, the molecular diagnosis, based on rDNA region sequencing, of several isolates primary named as Phomopsis vaccinii originating from Lithuania was carried out. Sequences of eight strains (Phomopsis vaccinii VAAT-PZ4, VAAT-PZ5, VAAT-PZ6, and VAAT-PZ11, Diaporthe eres VAAT-4.244 and VAAT-PZ8, Phomopsis sp. VAAT-PZ15 and BI-PH02B) were analysed by comparing with the accessions from GenBank.