This study analyzed the characteristics of reverse transcriptase sequences of copia-like retrotransposons in Amaranthus via PCR amplification and sequence approaches. The results are as follows: (1) The reverse transcriptase sequences of copia-like retrotransposons were detected in all 30 Amaranthus accessions studied, indicating that this class of retrotransposons is ubiquitous in Amaranthus; (2) Twenty-eight reverse transcriptases in A. quitensis were cloned and sequenced, showing extensive heterogeneity in base deletion mutation and stop codon mutation; (3) Cluster and alignment analyses of the 28 sequences and other published sequences of the reverse transcriptase from other species (such as rice, tomato and Drosophila) showed that the copia-like retrotransposons in A. quitensis have a close relationship with those in dicot and monocot plants. The evolution of copia-like retrotransposons in A. tricolor, which might be of the same origin as the copia and 1731 in Drosophila, was discussed.