Abstract: To elucidate the annual variation of foodborne pathogenic bacteria in commercially available shellfish, this study employed the plate spread method, complemented by PCR technology, to determine the total bacterial count and the levels of five foodborne bacteria in different tissues of Crassostrea hongkongensis and Perna viridis sourced from Haikou markets. The results indicated that: (1) Apart from Escherichia coli, the levels of other tested bacteria in C. hongkongensis and P. viridis mussels exhibited significant seasonal fluctuations. Specifically, the total bacterial count and Vibrio vulnificus peaked in August and September; Vibrio parahemolyticus levels in C. hongkongensis were higher in January and July, while those in P. viridis were higher in January and August; Listeria monocytogenes levels in C. hongkongensis were higher between June and August, and those in P. viridis peaked in June; Salmonella levels in C. hongkongensis were higher between May and July, whereas those in P. viridis were higher in July and August. (2) There were certain differences in the levels of foodborne bacteria between C. hongkongensis and P. viridis. For instance, in the months with high levels of E. coli, V. parahemolyticus, L. monocytogenes, and Salmonella, the bacterial counts detected in C. hongkongensis were higher than those in P. viridis (9.3×10⁴ CFU·g⁻¹ vs. 5.0×10⁴ CFU·g⁻¹, 7.9×10⁴ CFU·g⁻¹ vs. 6.1×10⁴ CFU·g⁻¹, 2.0×10⁵ CFU·g⁻¹ vs. 1.5×10⁵ CFU·g⁻¹, 5.7×10⁵ CFU·g⁻¹ vs. 3.8×10⁵ CFU·g⁻¹, respectively). Conversely, for V. vulnificus, the detection levels were higher in P. viridis (1.9×10⁵ CFU·g⁻¹ vs. 1.1×10⁵ CFU·g⁻¹). (3) The differences in the levels of different foodborne bacteria among the five tissues of the two shellfish species were relatively small, with slightly higher bacterial levels in the mantle and gills compared to other tissues. In summary, this study quantified the annual variation of foodborne bacteria in two commercially available bivalve species, providing data support for the safe consumption of oysters and mussels.