The aim of the study was to investigate the effect of the Schizochytrium limacinum marine algae on the fatty acid profile of goat milk, with particular reference to n-3 fatty acids, especially docosahexaenoic acid (DHA) and rumenic acid. Forty dairy goats were randomly allocated to four groups: C – fed with 1500 g alfalfa hay and 600 g concentrate; CMA – received the same forages and concentrate supplemented with 15 g/head/day microalgae; P – kept on pasture with 600 g concentrate; PMA – kept on pasture with 600 g concentrate with microalgae inclusion (15 g/head/day). The C and CMA groups were housed indoors, while the goats from P and PMA groups were kept on a natural pasture. The experiment lasted 31 days, including the last 10 days of sampling period. Marine algae feeding had no negative effect on milk yield and milk composition. The microalgae inclusion considerably increased DHA concentration in milk in both marine algae groups (0.40% in CMA and 0.39% in PMA), and additionally the n-6/n-3 ratio was also more favourable in the microalgae supplemented groups (1.25 and 1.37 in CMA and PMA groups, respectively) as compared to the C and P groups respectively in which this ratio was 2.30 and 1.44 (P < 0.01). Also, marine algae supplementation increased the concentration of rumenic acid (0.89% and 1.07% in CMA and PMA groups, respectively) in milk in comparison to C (0.46%) and P (0.77%) groups. So, it can be concluded that diet supplemented with microalgae significantly increased the concentration of beneficial fatty acids in goat milk.