BackgroundIsolate CH-1 of Rhizoctonia solani Kühn was commonly used in our studies of the pathogenicity and genetics of this pathogen. During the preparation of homokaryons through protoplast regeneration and tuft formation, a defective homokaryon was detected and a new variant was obtained.ResultsWhen tuft formation was used to identify the karyotic nature of single protoplast regenerants (SPRs) of Rhizoctonia solani AG1-IC isolate CH-1, one homokaryon type designated as A type and the parental heterokaryon designated as AB type were obtained. The homokaryon B type was not found. Various approaches were used to obtain SPRs, including from fast or slow growing protoplast regenerants, and from regenerants of protoplasts released from mycelia grown in different nutrient broths or at different temperatures. Without exception, all these SPRs were either homokaryon A or heterokaryon AB. Moreover, the SPRs obtained from different generations of SPRs, and from different generations of SPRs treated with lytic enzymes 3 to 4 times also were invariably either homokaryon A or heterokaryon AB. When single hyphal isolates were obtained from the tuft resulting from the pairing between homokaryon A and heterokaryon AB, only the heterokaryon and a variant were obtained. The variant did not form tuft when paired with parental heterokaryon AB or homokaryon A. Its protoplast regenerants gave rise to heterokaryon AB, homokaryon A and the variant, indicating that it is a new kind of heterokaryon.ConclusionInability to obtain homokaryon B despite numerous attempts suggests that the B type nuclei are probably defective and are dependent on A type nuclei for their multiplication. This is the first report of a heterokaryotic R. solani strain carrying a defective type of nuclei. A new variant which is a new kind of heterokaryon was obtained from the tuft resulting from the paring between the homokaryon A and the parental heterokaryon AB.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0069-z) contains supplementary material, which is available to authorized users.