The increasing demand for canola (Brassica napus) for both food (e.g. vegetable oil) and non-food (e.g. biofuel) applications presents significant socio-economic benefits. While genetic engineering offers great potential to speed up the process of canola improvement, such an effort relies on a good understanding of the molecular mechanisms underlying seed development, fatty acid (FA) metabolism, and oil content. Applying a well-defined algorithm to a time-series gene expression dataset of B. napus during seed development, and a well selected dataset of interactions between transcription factors and their target genes, we derive a dynamic regulatory map that is able to recover many of the known aspects of these responses. Predictions made in this study are further validated through literature search, leading to potential new roles for LEC1, LEC2, WRI1, FUS3, MYB30, and ABI3 in controlling B. napus seed development and FA metabolism related genes, thus potential targets for genetic improvement of oil production.