Cucurbit aphid-borne yellows virus (CABYV) causes yellowing symptoms on the older leaves of plants from several species in the Cucurbitaceae family. Previous phylogenetic analyses showed the existence of two major clades of CABYV isolates related to their geographic origin – Asian vs European-African (Mediterranean) groups. To provide an understanding of the molecular variability of CABYV in Turkey, surveys were performed in 2011 to 2015 to obtain plants infected by the virus in four provinces, where cucurbit cultivation is of economic importance for the country. One hundred and forty leaf samples of cucurbit plants showing virus-like symptoms: yellowing, mosaic, deformation on leaves and stunting, were collected from Antalya, Ankara and Burdur provinces during the 2011–2013 growing seasons and 40 leaf samples from Tokat province during the 2015 growing season. Five CABYV isolates, collected in Antalya, Hatay and Mugla provinces in 1994, were added to the analysis. The coat protein coding regions of 15 CABYV isolates were amplified by reverse transcription-polymerase chain reaction (RT-PCR) using specific primers and sequenced. According to the sequence analyses, 11 isolates shared 99% nucleotide identity with isolates from Egypt, Slovenia and Montenegro, three isolates showed more than 99% nucleotide identity with isolates from China, South Korea and Iran, and one isolate presented evidence of mixed infection. Neighbour-joining analyses based on the resultant sequences revealed that the Turkish CABYV isolates clustered in two distinct molecular groups: five isolates from 1994, six isolates from 2012–2013 and one from 2015 clustered in the Mediterranean group, whereas three isolates from 2012–2013 clustered in the Asian group. In addition, one isolate presented a mixed infection of the two groups.