Abstract: The previous molecular identification of a flowering time QTL segregating in the Arabidopsis Ler× Cvi cross, demonstrated that natural allelic variation at the blue light photoreceptor CRY2 gene affects flowering time El‐Assal et al., 2001). In addition, previous works on the same cross have mapped several QTL affecting other unrelated life history traits in the CRY2 genomic region. In the present report, we have used a set of Arabidopsis Ler transgenic plants carrying four different functional CRY2 transgenes for phenotypic analyses, with the aim of exploring the extent of pleiotropy of CRY2 allelic variation. It is concluded that previously identified QTL affecting fruit length, ovule number per fruit, and percentage of unfertilized ovules are caused by this same Ler/Cvi CRY2 allelic variation. In addition, dose effects of the CRY2‐Ler allele are detected for fruit length. A seed weight QTL at the map position of CRY2 could not be confirmed and also no effect on seed dormancy was observed. Thus, it is shown that transgenic plants carrying different alleles can be a useful tool to attribute QTL for different complex traits to a specific locus, even when the relationship among the traits has not been previously suggested.