Abstract: Rye (Secale cereal L.) is an important alien gene resources in wheat (Triticum aestivum L.) genetic research as it is a related species of Triticinae. It has been used in improving disease resistance, yield and grain quality of wheat. Molecular marker technique (a valuable tool in molecular biological research) has been used extensively in rye research. This review summarized the progress in research regarding the applications of molecular marker techniques in rye. Such techniques included genetic linkage map construction, valuable gene identification and mapping, and specific rye genome marker development and application. The application prospects of molecular marker techniques in rye research were also discussed.