A total of 500 samples, 100 of each milk, feed, swabs from milking equipment (milk tanks), drinking tanks swabs and dairy cows fecal swabs samples were collected from different small herds of apparently or subclinical dairy cattle in El-Kabotti and Bahr El-Baker zone at Port-Said Governorates during the period from September to December 2018. The samples were examined for isolation and identification of Salmonella species and E. coli with studied of their virulence and resistance gens and sequence of some genes. The results revealed that Salmonella species and E. coli could be detected in a percentage of 1.8% and 2.8% respectively from the examined samples. Salmonella isolates from the examined samples were identified biochemically and serological as S. Typhimurium S. Entiriditis and S. saintipaul with a percentage of 66.67% (6/9), 2.22% (2/9) and 11.11% (1/9) respectively, while that of E. coli were O26 (5/14), O119 (2/14), O125 (4/14), O126 (1/14) and O127 (2/14) with a percentage of 35.71%, 14.28%, 28.60%, 7.14% and 14.28% respectively. The isolated strains of Salmonella species (n=9) and E. coli stains (N=14) were investigated for antibiotic susceptibility profile to 10 antibacterial agents by disc diffusion method. The resistances of the isolated Salmonella and E. coli strains were ranged from a various degree of resistances to complete resistances (100%). By using conventional PCR, all Salmonella were harbored InvA, stn and bcfC genes while E. coli were harbored PhoA, TraT and fimH genes. The resistance genes that detected in Salmonella strains were ampC, mphA and aacC while that of E. coli were bltEm, ampC, mphA, Aada1 and aacC. The prevalence of the resistance genes were discussed. DNA sequencing of stn and bcfC genes for Salmonella and TraT and fimH genes for E. coli were discussed and compared with other strains in Gen Bank. The mutations in quinolone-resistance gene were studied by determining regions of the gyrA gene for Salmonella and E. coli. The public health hazards of these microorganisms as well as recommended measures to improve hygiene measures in dairy farms were discussed.