Symptoms resembling those caused by begomoviruses have been observed in common bean and other leguminous crops in Ecuador in the last few years. The only begomovirus species found infecting legumes (common bean and cowpea) in the country to date is Cabbage leaf curl virus. During May to June 2017, a survey of leguminous plants was conducted in the Ecuadorian localities of Santa Elena (Santa Elena province), Milagro (Guayas province), and Pallatanga (Chimborazo province). Twenty-four plants showing leaf deformation and/or mosaic symptoms were sampled, including common bean (Phaseolus vulgaris, n=21), soyabean (Glycine max, n=2), and pigeon pea (Cajanus cajan, n=1). Most common bean plants were infested with whiteflies (Aleyrodidae) that were also collected. Based on the results of polymerase chain reaction assay, rolling-circle amplification and sequence comparison, the causal agent was identified as Pepper leafroll virus (PepLRV). Based on the species/strain demarcation threshold for the viruses in the genus Begomovirus, the isolate characterized belongs to a new strain of PepLRV. DNA sequence analysis identified the whiteflies as Bemisia tabaci Middle East-Asia Minor 1 (MEAM1, formerly B biotype), which is known to be an efficient vector of begomoviruses. This is thought to be the first report of PepLRV in Ecuador and of soyabean as a host for the virus, which had been identified only in Peru to date. Also, this is thought to be the first molecular evidence of the presence of B. tabaci MEAM1 in the country.