The objective of this work was to investigate the fatty acid composition and assess hygienic quality of the Algerian camel milk from Targui breed, then to compare obtained results with cow milk in local rearing conditions. Sampling was performed over three months at a rate of one sample per month. The physicochemical analyzes carried out revealed that the Targui camel milk had averages values of 6.33 ± 0.15 for the pH, acidity equal to 18.50 ± 0.02 °D, and 1030.40 ± 1.08 for density. The total dry extract and the fat levels were lower than those of cow milk. In addition, results of fatty acid profile analysis from camel milk revealed a relatively low level of saturated fatty acids (SFAs) compared to cow milk, palmitic acid (C16:0) being the predominant fatty acid in both milks. The content of unsaturated fatty acids (UFAs) was significantly higher in camel milk fat compared with cow milk, with higher total monounsaturated fatty acids (MUFAs) rate in camel milk. Oleic acid (C18:1 n9) was in the same proportions, and the most abundant unsaturated fatty acid in both species. However, no significantly difference was observed between PUFAs levels of camel and cow milk. Linoleic acid (C18:2 n6) was the most represented polyunsaturated fatty acid in both milks with similar proportions. In contrast, the content of α-linolenic acid (C18:3 n3) was significantly (p<0.001) higher in cow milk than in camel one.