As the largest transposable element in the plant genome, retrotransposons are thought to be involved in citrus genetic instability and genome evolution, especially in sweet orange, which is prone to bud mutation. In the present study, the presence of copia-like retrotransposons, their heterogeneity, genomic distribution, and transcriptional activities in Citrus were investigated in 12 sweet orange (Citrus sinensis Osbeck) cultivars using a PCR assay designed to detect copia-like reverse transcriptase (RT)sequences. Twelve amplification products from each cultivar were cloned and sequenced. The cloned sequences showed great heterogeneity, except "Dream" navel and "Hamlin", both of which shared the same sequence. Frame shifting, termination, deletion, and substitution accounted for the heterogeneity of RT sequences. Southern blot hybridization using the RT1 clone from the "Cara Cara" navel as a probe showed that multiple copies were integrated throughout the sweet orange genomes, which made the retrotransposon possible an effective molecular marker to detect citrus evolution events and to reveal its relationship with bud mutation. No transcriptional activities of the retrotransposon were detected by RT-PCR and Northern analysis in the fruits and leaves of either "Cara Cara" or "Seike" navels.