Small ruminant's milk is recognized as one kind of nutritious food owed to its originality and medicinal values. 100 samples collected from raw ewe and goat milk (50 of each) reared in Assiut City, Egypt. Milk samples were screened for probiotics Lactobacillus, Bifidobactria and Enterococcus spp. as well as their differentiation especially those harboring bacteriocin genes. On the other hand, milk samples were tested for the existence of total aerobic bacteria and total coliforms. Goat's milk showed higher existence of total aerobic and total coliforms count more than ewe's milk which showed higher existence of Lactobacillus, Bifidobacteria and Enterococcus spp. The study detected Enterococcus faecium as more in ewe's milk (40%) than goat's milk (25%) and tested for harboring bacteriocin genes (mes Y &Plantaricin E/F). Our study concluded that goat's milk had more total pathogenic parameters than ewe's milk, but ewe's milk had more probiotic lactic acid bacteria (LAB); Lactobacillus, Bifidobactria and Enterococcus spp., also, contained Enterococcus faecium strains harboring bacteriocin genes mesY& Plantaricin E/F genes more than those of goat's milk. Both of them have its value and uses in dairy industry. Further studies are needed and caring produce of these types of milk and their products in Egypt and could be assessed in several models in a similar manner to what is studied with bovine milk.