Barley yellow dwarf virus (BYDVs) is an emerging threat for wheat and may seriously threaten its production, especially as climate change may result in increased infestation by aphids, the insect vectors of the virus. To assess the possibility of using pathogen‐derived resistance against the virus, the genetic diversity of BYDVs originating from different wheat‐growing areas of Pakistan where its incidence has been higher was investigated. Wheat samples with suspected symptoms of BYDVs were screened for the presence of Barley yellow dwarf and Cereal yellow dwarf viruses (B/CYDVs) subgroup 1 (Barley yellow dwarf virus‐PAV, BYDV‐MAV, BYDV‐SGV) and subgroup II (BYDV‐RPV, CYDV‐RPV, BYDV‐GPV) by PCR using basic multiplex oligonucleotides designed on coat protein (CP) of the virus. Of 37 samples tested, 13 were positive for BYDV subgroup I and only one sample was positive for BYDV subgroup II. Samples positive for subgroup I were further tested by PCR, and results showed that 10 samples were positive for BYDV‐PAV and three for BYDV‐MAV. DNA sequences of CP region of nine isolates (BYDV‐PAV) were determined and compared with available sequences in databases. Sequence analysis showed that three isolates (from Fatehjang, Nowshera and Attock districts) had maximum identity (92.8–94.6%) to BYDV‐PAS, and six isolates (from Peshawar, Islamabad Swabi and Faisalabad districts) had maximum identity (99.3–99.7%) to BYDV‐PAV. Thus BYDV‐PAV species may be dominant in northern wheat‐growing areas of Pakistan. The conserved nature of the BYDVs suggests that pathogen‐derived resistance strategies targeting the coat protein of the virus are likely to provide protection under field conditions.