An insertion/deletion polymorphism (Ind2) in the Brassica nigra CONSTANS LIKE 1 (Bni COL1) gene was previously found to be associated with variation in flowering time. In the present study we examine the inter-specific divergence of COL1 in the family Brassicaceae. Analysis of codon substitution models did not reveal evidence of positive Darwinian selection, but comparisons of the COL1 gene in different species revealed a surprising number of indels. A total of 24 indels were found in the 650 bp of the middle variable region of the gene. This high number of indels could reflect a lack of constraint on length of this region of the protein, or the effect of positive selection. The number of indels was close to that expected in non-coding DNA, but the indels were longer in COL1 than those observed in non-coding regions. Reconstruction of indel evolution indicated that most indels resulted from deletions rather than insertions. The Ind2 indel that has shown association with flowering time in Brassica nigra exhibited a remarkable distribution in the Brassicaceae family, indicating that the polymorphism may have persisted more than ten million years. Considering presumed historic populations sizes of Brassicaceae species, such a long persistence time seems unlikely for a neutral polymorphism.