The invention discloses a peach SSAP (Source Service Access Point) molecular marker primer combination, a peach SSAP molecular marker combination and an application of the peach SSAP molecular marker combination in analysis on the genetic diversity of peach varieties, wherein the peach SSAP molecular marker primer combination comprises an LTR (Long Terminal Repeat) primer, a selective amplification primer and a tail primer; the peach SSAP molecular marker combination comprises ten molecular markers JY01, JY02, JY03, JY04, JY05, JY06, JY07, JY08, JY09 and JY10. Due to the design of a peach retrotransposon LTR sequence primer, a selective amplification product is proved to be clear and abundant in amplification strip and have high efficiency, reliability and practicability through fluorescent capillary electrophoresis detection; in addition, a selective amplification PCR (Polymerase Chain Reaction) system is optimized, and a tail sequence is added, so that the traditional selective amplification PCR system is improved, and the cost for carrying out relevant researches by using the molecular markers is reduced. The SSAP molecular marker combination disclosed by the invention has relatively high polymorphism in the plurality of peach varieties, comprises stably existing markers and can be used for peach variety identification and genetic diversity analysis.