Abstract Background Salmonella is one of the most common and economically important zoonotic pathogens. This study aimed to determine the occurrence of Salmonella serovars in sheep and goats and their probable zoonotic risk to humans in Suez Canal area in Egypt. A total of 320 fecal samples from sheep (n = 120), goats (n = 100), and humans (n = 100) were collected and examined for the presence of Salmonella based on cultural and biochemical characteristics, and serological analysis. Moreover, the virulence of the identified Salmonella isolates was assessed by molecular screening for invA, stn, spvC, and sopB virulence genes using PCR. Results Overall, the occurrence of Salmonella in sheep feces (23.3%) was higher than that in goat feces (7%) and human stool (13%) in the study area. The identified isolates belonged to 12 serotypes; ten, five, and eight from sheep, goats, and humans, respectively. The most frequently identified serotypes were S. Typhimurium from sheep feces, and S. Enteritidis from both goat feces and human stool, with four serotypes; S. Typhimurium, S. Enteritidis, S. Dublin and S. Saintpaul, were mutually shared between all of them. Demographic data revealed that diarrheic sheep (85.7%) and goats (25%) had a higher risk for Salmonella fecal carriage than non-diarrheic ones (19.5% and 6.25%, respectively). The prevalence of Salmonella infection in humans in contact with sheep and goats (28%) was significantly higher than its prevalence in people having a history of contact with animals other than sheep and goats (10%) and those having no history of animal contact (7.3%) (χ2 = 6.728, P ˂ 0.05). The stn, spvC, and sopB genes were detected in 98.1% of the isolates, with a significant, very strong positive correlation for their mutual presence (P