Consumer awareness of the link between dietary fats and health outcomes has led to increased demand for food products enriched with bioactive fatty acids (FA). Ruminant-derived fats, such as dairy fats, contribute significantly to the American diet and contain many unique beneficial FA, such as short- and medium-chain FA, n-3 FA, conjugated linoleic acids (CLA), vaccenic acid (VA), as well as odd-and branched-chain FA (OBCFA). Increasing these FA in dairy products by altering farm management practices, such as breed, lactation stage, and nutrition, may improve human health without a change to the diet. The overarching goal of this dissertation was to evaluate on-farm strategies to increase the content of bioactive FA in bovine milk. The first objective was to enrich milk fat with bioactive FA via supplementation with echium oil, a terrestrial oil rich in n-3 FA. Treatments were 1.5% and 3.0% dry matter as lipid encapsulated echium oil (EEO) which were compared to a control (no EEO). Milk fat contents of n-3 FA increased with EEO supplementation but the transfer of n-3 FA from EEO into milk fat was rather low (< 5%). In a subsequent trial, ruminal protection of EEO and post-ruminal release of EEO-derived FA was examined. EEO-derived FA were preferentially incorporated into plasma lipid fractions unavailable to the mammary gland. Moreover, fecal excretion of EEO-derived FA ranged from 7-14% of intake, and VA and CLA, the biohydrogenation and metabolism products of n-3 FA, increased in milk and feces with EEO supplementation. Therefore, lipid-encapsulation provided inadequate digestibility and low transfer efficiency of n-3 FA into milk. The second objective was to compare the bacterial community structure and unique bioactive FA in bacterial membranes and milk fat between Holstein (HO), Jersey (JE), and HO x JE crossbreeds (CB) across a lactation. Lactation stage had a prominent effect on rumen bacterial taxa, with Firmicutes being most abundant during early lactation. The FA composition of bacterial cells was affected by both lactation stage and genetics, and OBCFA in bacterial cells were positively correlated with several bacteria of the Firmicutes phylum. HO and CB exhibited greater contents of various bioactive FA in milk than JE. The highest content of all bioactive FA occurred at early lactation, while OBCFA were highest at late lactation. The third objective was to determine the effects of grazing a monoculture vs. a diverse pasture on rumen bacterial and protozoal taxa, their membrane FA composition, and milk FA. Microbial communities shifted in response to grazing regime accompanied with changes in their membrane FA profiles. Rumen microbiota from cows grazing a diverse pasture had higher contents of n-3 FA and VA, but lower contents of OBCFA. Microbial membrane FA correlated with microbial taxa, the contents of ALA and n-3 FA were positively correlated with the bacterial genus Butyrivibrio and the protozoal genus Eudioplodinium. Milk contents of CLA and n-3 FA increased when cows grazed a diverse pasture, while grazing a monoculture led to greater milk contents of OBCFA. In conclusion, grazing cows on a diverse pasture, when compared to genetic effects and lipid supplementation, was the most efficacious strategy to increase the content of bioactive FA in milk.