Plant oils supplementation in animal diet has been used as a reliable feeding strategy to enhance omega-3 fatty acids content in milk toward increasing milk nutraceutical value. To investigate diet induced differences gene expression of milk protein LALBA and CSN2 and milk fat synthesis (CD36, XHD, ACACA, SCD and FABP3), linseed (Linum usitatissimum) and chia (Salvia hispanica) oils have been fed as additive at 1% of diet for 60 d to lactating goats (n = 12). The milk from Beetal goats (Capra aegagrus hircus) at d 0 (before treatment) and after treatment during 2 stages of lactation (d 15 and d 34) was collected. The milk fat, after centrifugation, was processed for total RNA isolation and subjected to gene expression analysis. The RNA quality (OD ratios) and quantity (concentration), as measured by NanoDrop spectrophotometer, did not differ (P > 0.05; 2-way ANOVA) either by treatments or by days in lactation. The mRNA expression of ACACA, FABP3 and CD36 at d 15 and SCD, XDH, LALBA and CSN2 at d 34 was upregulated at d 34, in comparison to d 0, as the main effects of stage of lactation. Supplementation of feed with both the oils increased (P < 0.05) expression of CD36 at d 34, with more pronounced expression by linseed. In relation to control, abundance of XDH was increased on d 34 (18-fold; P < 0.01) in linseed oil fed milk. However, abundance of milk protein genes was not affected by the treatment (P > 0.05), indicating that milk production is unlikely affected by oil supplementation. There were statistically significant interactions observed among all the genes of our study with the lactation stage. Data suggest that linseed supplementation is more effective in increasing gene expression of milk fat synthesis genes than chia oil. Since the percent of omega-3 fatty acids in milk of linseed oil fed animals is more (1.26) than the chia oil (0.95), indicating that linseed oil could be a choice for fatty acid augmentation in milk.