Rhizoctonia isolates isolated from plant and soil samples collected from Central Anatolian wheat fields were subjected to PCR-RFLP and DNA sequence analysis using MseI, Ava II/HincII, MunI, MspI (HapII), HinfI, EcoRI, HaeIII, HinfI and HhaI enzymes. As a result of the analysis, Rhizoctonia isolates were determined to be multinucleate Rhizoctonia solani AG 2-1, AG 2 BI, AG 3, AG 4 HG II, AG 5, AG 8, and Waitea circinata var. circinata, Waitea circinata var. zeae, Waitea circinata var. oryzae group I, binucleate Rhizoctonia AG DI, AG E, AG G, AG I and AG K. Isolates in the same group and subgroup in phylogenetic trees were in the same group. Isolates from different groups and subgroups were located in various branches, revealing the genetic differences between the groups and subgroups.