The invention discloses a rhizoctonia solani kuha SSR mark, as well as a preparation method and application thereof, and belongs to the technical field of molecular organism. The rhizoctonia solani kuha SSR mark comprises 8 groups of primer pairs, and the preparation method comprises the following steps: firstly, extracting genome DNA of rhizoctonia solani kuha; secondly, obtaining a DNA fragment through restriction enzyme digestion total NDA; thirdly, ensuring that a biotin labeled probe is cross-fertilized with a target fragment; fourthly, enriching a DNA fragment containing an SSR sequence through a magnetic bead; fifthly, amplifying and purifying the DNA fragment containing the SSR sequence; sixthly, performing clone sequencing on the DNA fragment; seventhly, designing an SSR primer through an SSR flanking sequence, which is used for amplifying a microsatellite fragment of a locus. The rhizoctonia solani kuha SSR mark is high in primer specificity, stable in amplification, simple in operation, short in period and low in cost, meanwhile has the advantages of rich codominant inheritance and polymorphism, and can be applied to analysis of the genetic diversity of rhizoctonia solani kuha.