Based on the citrus genome information，this study developed a molecular technology based on the transposon sequences to distinguish bud mutants in citrus. Transposon display（TD） technology was used to investigate the transposon polymorphisms of 43 citrus bud mutant cultivars and 7 wild type citrus cultivars. The results showed that 5 DNA transposons（DTM63，DTM58，Helitron1，Spem and mPing2）and 4 retrotransposons（Line1，LTR-Gypsy3，LTR-Gypsy5 and Tcs2）could clearly identify the differences between bud mutants. Robertson navel orange and its early-maturing cultivar Robertson 35 could be identified by DTM63，Spem and mPing2；mPing2 could identify 4 pairs of bud mutants as following：Robertson navel orange and Robertson 35，Anliu and Hong Anliu，the common ponkan and Qianyang seedless ponkan，red flesh and orange skin of Guanxi pummelo. DTH3，a DNA transposon，was highly polymorphic among sweet oranges，and it could identify different bud mutants in sweet orange. Therefore，TD is a type of noticeable and effective molecular marker technology in the identification of citrus bud mutants.