The study aimed at identifying the pathogen associated with passionfruit woodiness disease in Rwanda. Field work was conducted in Rwanda while, laboratory aspects were carried out in Biosciences for eastern and central Africa-International Livestock Research Institute Hub, Nairobi, Kenya. Duration of the study was from September 2012 to May 2013. Two hundred and one leaf samples exhibiting virus-like symptoms were collected from farmer’s fields in Nyamagabe, Ngororero and Gicumbi district found in South, West and North provinces of Rwanda, respectively. Virus detection was done using enzyme-linked immunosorbent assay and reverse-transcription polymerase chain reaction. Virus-like symptoms observed in the field included; leaf mosaic, crinkle, distortion, fruit woodiness and malformations. Ugandan passiflora virus was detected in 70% of the positive samples and other unidentified potyviruses. The incidence of virus infection was highest in North at 45.8% and lowest in West province at 18.7%. Partial amino acid sequences of the coat protein of 169 residues were used to determine the identity of the associated virus. Sequences obtained were highly similar and displayed features typical of potyviruses with 93-100% identity. Comparisons of these sequences with those of other existing potyviruses indicated highest identity (94-100%) to Ugandan passiflora virus isolates from Uganda. Sequences of four Rwandan isolates are deposited in Genbank: isolate RW10 (Accession No. MK132862), RW23 (MK132863), RW104 (MK132864) and RW140 (MK132865). This study confirms presence of the Ugandan passiflora virus in the country. This necessitates the need for production and use of virus-free planting materials, development of virus resistant genotypes and adoption of efficient seed certification systems.