Goat milk and dairy products are an important nutritional and economic resource in Tropics. However, the yearly production of milk is affected by the scarcity of pastures during the dry season, which leads to seasonal weight loss (SWL) in ruminants. The aim of the work is to identify physiological markers indicative of SWL tolerance in 2 dairy goat breeds, with different SWL tolerance levels. The results will help to define breed selection strategies in drought prone regions. Nuclear magnetic resonance (NMR) was used to compare the observable metabolome present in aqueous extracts of mammary glands and milk serum from 2 dairy goat breeds; tolerant to dry environment (Majorera) and susceptible (Palmera). Ten Palmera and 9 Majorera dairy goats in mid lactation were used in this study. Animals were divided in 4 experimental groups (Majorera control, Palmera control, Majorera restricted and Palmera restricted). Milk samples were collected daily, after milking from the whole available milk, and mammary gland biopsies were collected after 23 d. Aqueous fractions were obtained by tissue aqueous/organic extraction and milk serum was obtained by ultra-centrifugation. We collected ¹H NMR spectra (1D-NOESY and CPMG) from the aqueous extract of the mammary gland, and the milk serum. ¹H NMR Spectrum deconvolution was used for metabolite profiling analysis and has led to the identification of 47 compounds in the aqueous fraction of mammary gland extracts. Lactose, glutamate, glycine, lactate and glucose were found to be the most abundant. Statistical evaluation using principal component analysis (PCA) and partial least squares (PLS) revealed differences between control and restricted animals, although no differences between breeds were observed. Preliminary profiling analysis of milk serum samples resulted in the identification of 20 metabolites.