The current study investigated the effects of the supplementation of lambs with algae on the expression of genes that direct the accumulation of long chain omega-3 polyunsaturated fatty acids (LCn-3PUFA). The nutrition of the lamb's dam around mating was also considered. The dams were fed with either silage (SLG) or oat/cottonseed (OAT) based diets for six weeks prior to and, three weeks following conception. mRNA levels of FADS1, FADS2, CPT1, SCD, ACC and fad2 were measured in the liver, muscle and subcutaneous fat from lambs fed a control diet consisting of oat and lupin grains and chopped lucerne (CTRL) or the CTRL diet with algae (DHAgold™) added at 1.92% DM (ALG). The lambs were 117.4±2.4 days of age and weighed 37.3±3.2 kg at the beginning of the experimental period, and six weeks later they were slaughtered at 160.4±2.4 days of age and a final live weight of 50.1±4.4 kg. The expression of FADS1 in liver tissue was not affected (P>0.05) by the interaction between dam nutrition and algae supplementation, however it was higher (P<0.05) when lambs received the ALG diet compared with the CTRL and when their dams were fed SLG compared with OAT diet. The expression of FADS1 in muscle was negatively correlated (P<0.05) with the concentration of 20:4n-6, 20:5n-3 and 22:4n-6. The expression of FADS1, FADS2, SCD and ACC genes in lamb muscle was differentially affected by dam nutrition with the highest levels for the SLG+ALG treatment (P<0.05) compared with other treatments. The expression of SCD gene was not affected (P>0.05) by algae supplementation, but it was higher (P<0.05) when dams were fed SLG compared with OAT, however ACC was not affected (P>0.05).