Objective: To determine the effects of the water quality of Manila Bay on allometric parameters and histological biomarkers of selected organs of Pa viridis (P. viridis). Methods: Green mussels were collected from two coastal sites of Manila Bay, Las Pi?as–Para?aque (LPP) and Bacoor, Cavite (BC). Twenty-four green mussels from each site were used for the assessment of allometric parameters, and six green mussels from LPP and eight from BC were used for the assessment of histological structures of gonads, gut, and digestive glands. Gonad development were categorized into five stages, whereas gut and digestive glands were scored into four categories. Results: Allometric parameters that include shell height, weight, and total wet and dry soft tissue weight were significantly different between LPP and BC. It was also observed that exposure to the pollutants in Manila Bay resulted to delays in gonadal development, and detrimental changes and lesions in the histostructure of digestive gland and gut. Conclusions: Pollutants in Manila Bay have detrimental effects to the growth, reproductive development, and histological structure of digestive organs of P. viridis.