Copy number of a copia-like retrotransposon was compared in self- and cross-fertilizing taxa of the annual plant genus, Amsinckia. It was hypothesized that variation in copy number between populations with contrasting mating systems could be used to interpret the relative importance of factors influencing copy number (purging of element-induced mutations, ectopic exchange, and the level of heterozygosity). Populations of Amsinckia spectabilis var. microcarpa and A. furcata, two outcrossing taxa, and their self-fertilizing relatives, A. spectabilis var. spectabilis and A. vernicosa were studied. Probes for Southern hybridisation were generated for each respective taxa through the amplification of a conserved region of the retrotransposon sequence. There were no observable differences in the numbers or patterns of hybridised bands between related self- and cross-fertilizing taxa. The retrotransposon family studied may have been inactive before divergence of Amsinckia taxa, or the factors influencing copy number and genome location may be expressed in such a way as to yield no observable differences in copy number between species with contrasting mating systems.