The research deals with the study on milk yield and quality, with regard to fatty acid composition and some bio-nutritional molecules, linoleic acid isomers (CLA) and lactoferrin in milk from two Molise endangered goat populations, Montefalcone and Valfortorina. The experiment, lasted 7 months, was performed oil 60 lactating goats from the two populations. The following measurements were carried out on milk: milk yield and quality, fatty acid composition, two linoleic acid isomers conjugates (cis trans and trans, cis12), and lactoferrin content. Milk yield was about 275.6 and 258.3 kg for Montefalcone and Valfortorina goat. Milk quality was good for protein (3.64 and 3.59%) and fat (4.46 and 3.97%) in both the ethnic groups. PUFA and MUFA have statistically increased during the trial instead SFA has decreased. CLA concentration was, on average, 0.80 and 0.78% for Montefalcone and Valfortorina goat respectively. Lactoferrin content during lactation was 34.16 mu g/ml and 44.72 mu g/ml in Montefalcone and Valfortorina goat, respectively. The autochthonous types genetic safeguard, well-being in the native lands and traditionally reared, is necessary to conserve the productive peculiarity of populations at risk of extinction and valorize marginal areas with scarce productivity.