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Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci inBrassica rapaplants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genesFLCandSOC1(BrFLCandBrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, withFLCrepressing andSOC1promoting flowering. InB. rapa, there are four copies ofFLCand three ofSOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression ofBrSOC1paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in theBrSOC1paralogsBr004928, Br00393andBr009324, although the difference was not significant inBr009324. Thus expression of at least 2 of the 3BrSOC1orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of theBrSOC1orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For theBrFLCorthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus theBrFLCorthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.