The objective was to evaluate the effect of algae supplementation on milk fatty acid profile in lactating dairy goats. Eight multiparous Xinong Saanen dairy goats in late lactation (3.9 ± 0.4 Parities; 208.5 ± 2.7 DIM; 61.5 ± 6.2 kg BW) were randomly assigned to a replicated 4 × 4 Latin square design with 4 periods of 18 d. Goats were individually fed the basal diet with no algae (control), or basal diet supplemented with 10 (Alg-10), 20 (Alg-20) or 40 (Alg-40) g/goat of algae powder (Alltech Inc., Beijing, China) daily. Basal diet (forage: concentrate = 60: 40, DM basis) consisted of corn silage, alfalfa hay and concentrate was offered at 2 feedings (0830 and 1530) for 2 wk of acclimation before 4 experimental periods of 18 d. One hundred grams of concentrate was mixed with algae, and half of the mixture was offered before each feeding to guarantee all algae was consumed by goats during the experimental period. Milk fatty acid composition was analyzed on d 15 of each 18 d-period. Data were run by GLM procedure (SAS 9.2) and treatment means were compared by LSD test (P < 0.05). Fat- and protein-corrected milk (FPCM) yield was not affected by treatment. Further analysis on milk fatty acid composition showed that both MUFA and PUFA were changed with algae supplementation (P < 0.05). Higher concentration of C18:1n-9 trans and C20:1n-9 trans in milk for goats fed Alg-20 and Alg-40 diet was observed than those for goats fed control and Alg-10 diet (P < 0.05). Compared with control diet, experimental diets supplemented with algae induced increased concentration of C18:3n-3 and C18:3n-6 in milk. Moreover, increased responses in milk DHA and EPA were observed for treatment supplemented algae (P < 0.05). In conclusion, algae supplementation in lactating goat can change milk fatty acid composition, and indicated the potential to enhance some of the nutritionally healthy fatty acids in dairy goat milk.