In Maputo, Mozambique marine bivalves considerably contribute to the diet of the population. This study aimed to investigate seasonal distribution of Escherichia coli and Salmonella in clams from Maputo Bay, and examine their pathogenesis and antibiotic-resistant patterns. Standard multiple tube method revealed that the concentration of coliforms in all samples exceeded the limit for direct consumption, according to EU standards. Thirty-eight percent of the samples contained >60,000 MPN per 100 gram flesh. The occurrence of E. coli did not differ significantly due to season, while Salmonella was present in 100% of the samples during the rainy period and only in 30% during the dry. Multiplex polymerase chain reaction showed that 45% of E. coli isolates were positive for the virulent indicator gene fimA. The Salmonella isolates were identified as S. enterica serovar Typhimurium. Among other isolated coliformic Enterobacteriaceae, Shigella sp. (specie), which in low doses can cause severe gastrointestinal infections, was identified. Antimicrobial susceptibility, recorded by the disk diffusion method, showed resistance to the most commonly used antibiotics. This high levels of faecal contaminants in the clams points out the need for risk assessment and sanitary improvements.