Linseed oil is rich in the health promoting fatty acids, alpha-linolenic acid (omega-3) and oleic acid (omega-9), and is increasingly being used as a nutraceutical. However, there is limited linseed production in Kenya today, necessitating an increase in its production while ensuring a high content of the two fatty acids. This study aimed to determine the oil content and fatty acid profiles of five linseed varieties grown in a relatively warmer location, Juja, with that grown in a cooler location, Njoro, in two seasons (February-June and July-December); as well as the effect of nitrogen fertilizer application on linseed oil contents and fatty acid profiles. Mean oil content was slightly but significantly higher (p < 0.05) in Juja than in Njoro (34.8% versus 32.5 %, respectively). Mean oleic acid content was significantly higher in Juja (24.2 %) than Njoro (19.0 %), while alpha-linolenic acid was significantly higher in Njoro (48.5%) than Juja (44.2%). There were inter-varietal differences in both oil content and fatty acid profiles, and the significance of these differences were both season and location-dependent. Nitrogen fertilizer application had minimal effect on oil contents and fatty acid profiles. In conclusion, good quality linseed can be produced in both agro-ecological locations.