Isolates (a total of 129) of Rhizoctonia solani were collected from black scurf on potato tubers from different potato-growing regions in New Zealand. Sequence analysis of the nuclear ribosomal DNA internal transcribed spacer (rDNA–ITS) regions from these isolates identified three anastomosis groups (AGs), AG-3PT, AG-2-1 and AG-5. Isolates classified as AG-3PT were widely distributed, whereas AG-2-1 and AG-5 were confined to distinct locations. Sequence heterogeneity was identified in the ITS regions of 100 AG-3PT and AG-2-1 isolates. Variation in the sequence and length of the rDNA–IGS1 region was also observed for selected isolates of AG-3PT and AG-2-1. Phylogenetic studies found all AG-2-1 isolates belong to AG-2Nt, a subset of AG-2-1 previously associated with solanaceous crops in other countries. AG-2-1 isolates were consistently more aggressive than those of AG-3PT. Delayed emergence, severe infection on stolons, formation of aerial tubers and considerable yield losses were associated with AG-2-1, but they caused negligible black scurf. In contrast, AG-3PT caused black scurf on progeny tubers but variable effects on stem emergence and stolons. Furthermore, AG-2-1 isolates caused severe tuber malformation, but isolates of other AGs did not. This is the first report on the AG composition, genetic variability and pathogenicity of R. solani isolates associated with black scurf of New Zealand potatoes.