Diarrhea is one of the most common fatal disease of neonatal calves regardless of farm welfare. What makes treatment of these cases challenging is the increase in the incidence of multi-drug resistant bacteria, including E. coli and Salmonella. To isolate, identify, molecular characterize of E. coli and salmonella in diarrheic calves, 50 fecal samples were collected and analyzed aseptically. The preliminary result showed that 62% and 14% samples were positive for E. coli and salmonella respectively. Among the E.coli isolates O86:K59, O128:K-, O55:K59 (2), O86:K61, O119:K58, O08:K61, O126:K71 serotypes was detected in eight isolates while one isolate was untypeable. Three salmonella serotypes, Salmonella Typhimurium, Salmonella Anatum and Salmonella Florida was detected in the isolated samples . All of the E. coli strains had eaeA genes while 16.7 and 11.1% of them harbored stx1 and stx2 genes respectively. About 71.4% of salmonella isolates were positive for all five pathogenicity island genes from SPI-1 to SPI-5, while SPI-1, SPI-2 and SPI-5 were detected in 14.3% and SPI-2, SPI-3, SPI-4 and SPI-5 were positive in 14.3%. All E. coli strains were resistant to Ampicillin, Amoxicillin/Clavulanic, Cefazolin and Aztreonam., and all Salmonella serovars were resistant to Cefazolin, Chloramphenicol, Gentamycin, Kanamycin and Aztreonam. The present study identified multidrug resistant E. coli and salmonella as the common pathogen of calf diarrhea in the study area and the pathogens harbored common virulence markers of human diarrheic strains which might cause a food borne outbreak in the future.