Two repeated DNA sequences, pHaS13 and pHaS211, which revealed similarity to the int gene of Ty3-gypsy retrotransposons and the RNAse-H gene of Ty1-copia retroelements, respectively, were surveyed in Asteraceae species and within the genus Helianthus. Southern analysis of the genome of selected Asteraceae that belong to different tribes showed that pHaS13- and pHaS211-related subfamilies of gypsy- and copia-like retroelements are highly redundant only in Helianthus and, to a lesser extent, in Tithonia, a Helianthus strict relative. However, under low stringency posthybridization washes, bands were observed in almost all the other Asteraceae tested when pHaS13 was used as a probe, and in several species when pHaS211 was hybridized. FISH analysis of pHaS13 or pHaS211 probes was performed in species in which labelling was observed in Southern hybridizations carried out under high stringency conditions (Helianthus annuus, Tithonia rotundifolia, Ageratum spp., Leontopodium spp., Senecio vulgaris for pHaS13, and H. annuus, Tithonia rotundifolia, and S. vulgaris for pHaS211). Scattered labelling was observed over all metaphase chromosomes, indicating a large dispersal of both Ty3-gypsy- and Ty1-copia-like retroelements. However, preferential localization of Ty3-gypsy-like sequences at centromeric chromosome regions was observed in all of the species studies but one, even in species in which pHaS13-related elements are poorly represented. Ty1-copia-like sequences showed preferential localization at the chromosome ends only in H. annuus. To study the evolution of gypsy- and copia-like retrotransposons in Helianthus, cladograms were built based on the Southern blot hybridization patterns of pHaS13 or pHaS211 sequences to DNA digests of several species of this genus. Both cladograms agree in splitting the genomes studied into annuals and perennials. Differences that occurred within the clades of perennial and annual species between gypsy- and copia-like retroelements indicated that these retrotransposons were differentially active during Helianthus speciation, suggesting that the evolution of the 2 retroelement families was, within limits, independent.