The CONSTANS-like gene family has been shown to evolve exceptionally fast in Brassicaceae. In the present study we analyzed sequence polymorphism and divergence of three genes from this family: COL1 (CONSTANS-LIKE 1) and two copies of CO (CONSTANS), COa and COb, in B. nigra. There was a significant fourfold difference in overall nucleotide diversity among the three genes, with BniCOb having twice as much variation as BniCOL1, which in turn was twice as variable as BniCOa. The ratio of nonsynonymous-to-synonymous substitutions (dN/dS) was high for all three genes, confirming previous studies. While we did not detect evidence of selection at BniCOa and BniCOb, there was a significant excess of polymorphic synonymous mutations in a McDonald-Kreitman test comparing COL1 in B. nigra and A. thaliana. This is apparently the result of an increase in selective constraint on COL1 in B. nigra combined with a decrease in A. thaliana. In conclusion, a complex scenario involving both demography and selection seems to have shaped the pattern of polymorphism at the three genes.