We have used the polymerase chain reaction to analyze copia-like retrotransposons in the Egyptian cotton and its progenitors. All three cotton species studied contain reverse transcriptase fragments from copia-like retrotransposons. Sequence analysis of these reverse transcriptase fragments reveals that each is different from the others, with predicted amino acid diversities between 9 and 94%. The detection of stop codons and insertions/deletions in the derived amino acid sequences of the Gossypium RT clones, suggests that these clones represent defective retrotransposons. The presence of these sequences in G. barbadense progenitors, however, suggests the presence of active retrotransposons capable of producing new functional copies at an appropriate rate to compensate for the mutational loss of old ones. Phylogenetic analysis provided strong bootstrap support for a monophyletic origin of plant copia-like retrotransposons, yet showed high diversity within all species. Our results suggest that both vertical transmission of copia-like retrotransposons within G. barbadense lineages, and horizontal transmission between G. barbadense and its progenitors have played major roles in the evolution of copia-like retrotransposons in Gossypium.