Methane emissions by dairy cows have become a major issue as it has been suggested as a major contributor to global warming. In this paper, the methane emissions of 40 Jersey and 62 Fleckvieh x Jersey (FxJ) cows were predicted using specific milk fatty acids (FAs). Cows were on kikuyu pasture supplemented during pasture shortages with a replacement mixture consisting of lucerne hay, oat hay and soybean meal. All cows received the same concentrate mixture twice a day after milking at 7 kg per cow per day. Milk samples collected every 35 days over the lactation period, starting from 10 days after calving, were analysed by gas chromatography. Predicted methane emissions varied between breeds although differences were small (P>0.05). Using Methane equation 2 and 3, predicted methane emissions for Jersey and FxJ cows were 26.2±1.07 and 25.8±0.94 and 24.6±0.99 and 24.4±1.08 g/kg feed DM, respectively. Methane emissions in both breeds showed curvilinear (P<0.05) trends over the lactation period. Over all cows, lactation stages and breeds, the coefficient of variation in predicted methane emissions for Jersey and FxJ cows was approximately 20% possibly indicating genetic variation among cows. This variation could be used towards reducing methane production in dairy cows.