Rhizoctonia spp. anastomosis groups (AGs) associated with canola and lupin in the southern and western production areas of the Western Cape province of South Africa were recovered during the 2006 and 2007 growing seasons and identified using sequence analyses of the rDNA internal transcribed spacer regions. The effect of crop rotation systems and tillage practices on the recovery of Rhizoctonia spp. was evaluated at Tygerhoek (southern Cape, Riviersonderend) and Langgewens (western Cape, Moorreesburg) experimental farms. Isolations were conducted from canola planted after barley, medic/clover mixture and wheat, and lupin planted after barley and wheat, with sampling at the seedling, mid-season and seedpod growth stages. In the 2006 study, 93.5% of the Rhizoctonia isolates recovered were binucleate and 6.5% multinucleate; in 2007, 72.8% were binucleate and 27.2% were multinucleate. The most abundant AGs within the population recovered included A, Bo, I and K, among binucleate isolates and 2-1, 2-2 and 11 among multinucleate isolates. Crop rotation sequence, tillage and plant growth stage at sampling all affected the incidence of recovery of Rhizoctonia, but certain effects were site-specific. The binucleate group was more frequently isolated from lupin and the multinucleate group from canola. AG-2-1 was only isolated from canola and AG-11 only from lupin. This study showed that important Rhizoctonia AGs such as AG-2-1, 2-2 and 11 occur in both the southern and the western production areas of the Western Cape province and that crop rotation consistently influences the incidence and composition of the Rhizoctonia community recovered from the cropping system.