Previous work had shown that an intronless FLM cDNA expressed from a FLM promoter fragment was unable to rescue the flm mutant phenotype. Since this suggested that important information for FLM expression may reside in FLM non-coding sequences, we examined non-coding sequence polymorphisms with a potential role in controlling FLM expression and splicing. Using phylogenetic footprinting, we found conserved FLM promoter and intron 1 regions essential for FLM expression. By association analysis using polymorphism data from ≈800 Arabidopsis accessions, we identified a small polymorphic region in the FLM promoter and a highly polymorphic nucleotide triplet in FLM intron 6 controlling basal and temperature-dependent FLM expression. Small changes in the relative abundance of the FLM-ß splice variant dynamically modulated flowering at 15°C over a range of 15 leaves. When tested in a homogenous genetic background, FLM abundance correlated almost perfectly with flowering time (R2 = 0.94) and contributed (R2 = 0.21) to flowering time variation in heterogeneous natural Arabidopsis populations. Our data suggest that FLM-ß is an important determinant of flowering during cool or warm spring periods.