Sweet lime split bark is a disorder of increasing importance in Fars province. Previously we showed that a new variant of hop stunt viroid (HSVd-sb) was related to the disorder. It had homology with a noncachexia variant of hop stunt viroid (CVd-IIa-117) which causes cracking the bark of trifoliate orange rootstocks. In this study, showed that M.NgoBIX, BglI and BsrI restriction enzymes can cut HSVd-sb according to putative RFLP analysis using Vector NTI program (version 9.0.0) database but these restriction enzymes can’t cut CVd-IIa-117. In other hand some restriction enzymes can cut CVd-IIa-117 but can’t cut HSVd-sb. Therefore these two variants can be recognized by these restriction enzymes.