Due to the immense utilization in food and industry, there is enormous commercial and scientific interest to manipulate canola (Brassica napus L.) seed oil. Seed oil accretions are influenced by genes involved in embryo and seed development. FUSCA3 (FUS3) and LEAFY COTYLEDON1 (LEC1) are well-known transcription factors involved during seed and embryo development. The main objective of this project was to evaluate the role of these genes during seed storage deposition and microspore-derived embryogenesis in B. napus. For this purpose, six BnLEC1 transgenic lines and three BnFUS3 TILLING mutant lines were generated. The over expression of BnLEC1 significantly increased the seed oil content, while the down regulation of BnLEC1 or mutation of BnFUS3 reduced the level of seed oil. Experimental alterations of BnLEC1 and BnFUS3 triggered transcriptional modifications in enzymes taking part in sucrose transport and metabolism, glycolysis, and fatty acid (FA) biosynthesis. These changes are suggestive of a greater carbon pool to FA biosynthesis in tissues over-expressing BnLEC1, and a reduced carbon flux available for the synthesis of FA in BnLEC1 down regulators and BnFUS3 tilling mutants. While the elevated oil content induced by BnLEC1 was not accompanied by alterations in FA composition, oil nutritional value, or glucosinolate (GLS) levels, suppression of BnLEC1 reduced seed oil accumulation and raised levels of GLS, possibly through the transcriptional regulation of BnST5a (Sulphotransferase5a), the last GLS biosynthetic enzyme. BnFUS3 tilling mutant seeds had increased levels of linoleic acid, possibly due to the reduced expression of ω-3 FA DESATURASE (FAD3). The effects of altered expression of BnLEC1 and BnFUS3 were also assessed during microspore-derived embryogenesis. Substantial structural abnormalities, accompanied by changes in transcript levels of several embryo marker genes were observed in embryos in which the expression of BnLEC1 or BnFUS3 was altered. The changes in oil level and FA profiles observed in the transformed microspore-derived embryos followed a similar trend to that described in seeds. Collectively, these observations suggest that manipulation of BnLEC1 and BnFUS3 can be employed as a tool to enhance seed oil production and quality in B. napus.