Molecular epidemiology at local scale in Sicily (Italy) of ampicillin resistance in Salmonella spp. isolates from municipal wastewater (n = 64) and clinical specimens (n = 274) is described in comparison with previously examined Escherichia coli isolates (n = 273) from wastewater. High prevalence of antibiotic resistance (28.9%) with highest resistance rates against ampicillin (22.7%) was observed in E. coli isolates. Different resistance rates were observed in Salmonella according to the serovars, with prevalences of the same order in both wastewater and clinical isolates belonging to the same serovar (e.g., 91.7% ampicillin resistance in wastewater isolates vs. 70.8% in clinical isolates of the Salmonella serovar Typhimurium and 0% ampicillin resistance in both wastewater and clinical isolates of the Salmonella serovar Enteritidis). The beta-lactam resistance gene bla(TEM) was present in both wastewater and clinical Salmonella spp. isolates, with the exception of Salmonella enterica serovar Typhimurium isolates with a typical six-drug resistance pattern AmpChlSulTeStrSp that had the bla(PSE-1) gene. The bla(TEM) gene was present in all the E. coli isolates but one had the bla(SHV) gene. Several E. coli and some Salmonella isolates were positive for class 1 integrons with variable regions of 1.0 or 1.5 kb containing aadA1, dfrA17-aadA5, or dfrA1-aadA1 gene cassettes, whereas Salmonella serovar Typhimurium isolates with the six-drug resistance pattern were positive for both 1.0 and 1.2 kb integrons. Polymerase chain reaction replicon typing demonstrated the presence of multireplicon resistance plasmids in several isolates of E. coli, containing two to four of the replicons IncF, IncI1, IncFIA, and IncFIB, whereas other isolates showed resistance plasmids with only IncF, IncP, or IncK replicons. Replicon IncI1 was detected in one Salmonella isolate, whereas other isolates belonging to different serovars had IncN replicons. Analysis of isolates from wastewater can be a useful epidemiologic tool to monitor the prevalence of antibiotic resistance and genetic elements related to antibiotic resistance in Salmonella clones circulating in the human population.