Beet necrotic yellow vein virus (BNYVV) causes rhizomania which is one of the most devastating diseases in sugar beet fields worldwide. BNYVV symptoms were observed in Rz1-resistant sugar beet plants in a number of fields in Aksaray and Konya Provinces during surveys in 2011. Seven soil samples, taken from problematic areas in these provinces and known to be infested with populations of Polymyxa betae Keskin carrying BNYVV, were used in bait plant and molecular studies. Initially, the presence of other soil-borne viruses was investigated by using ELISA and RT-PCR. It was determined that BNYVV was in co-infections with pomoviruses, namely beet soil-borne virus and/or beet virus Q. The partial RNA-3 segment of BNYVV was amplified by RT-PCR, and the nucleotide sequences involving the p25 coding region were obtained. The deduced amino acid (aa) sequences of the p25 protein indicated that four BNYVV populations had 'ACHG' or 'VHHG' residues at positions 67-70. In addition, three populations containing three nucleotide deletions, not shifting the reading frame but affecting the aa at position 67 (-DHG) or 68 (D-HG), were identified. A deleted form of the p25 was identified in both the A-and J-type BNYVV populations. The pathogenicities of these BNYVV populations in the sugar beet genotypes rz1 and Rz1 were investigated under controlled conditions. All seven BNYVV isolates were capable of overcoming Rz1 resistance. These results seem to indicate that mutants of BNYVV with a deletion are aggressive, as are the isolates without deletion. Resistant beet cultivars will most likely be more productive in the future if these isolates become widespread in Turkey.