In the present study, the relationship between bacteria and phytoplankton in tropical coastal waters was investigated. The bacterial abundance, bacterial production, chlorophyll a concentration and net primary production were measured at several locations in the coastal waters of Peninsular Malaysia. Chlorophyll a concentration ranged from 0.40 to 32.81 μg L^–1, whereas bacterial abundance ranged from 0.1 to 97.5 × 10⁶ cells mL^–1. Net primary production ranged from 8.49 to 55.95 μg C L^–1 h^–1, whereas bacterial production ranged from 0.17 to 70.66 μg C L^–1 h^–1. In the present study, the carbon conversion factor used to convert bacterial production (cells mL^–1 h^–1) into carbon units ranged from 10 to 32.8 fg C cell^–1, and was estimated from the bacterial size distribution measured at each location. Both phototrophic and heterotrophic biomass (bacteria–chlorophyll a) and activity (bacterial production–net primary production) were significantly correlated, although their correlation coefficients (r²) were relatively low (r² = 0.188 and r² = 0.218 respectively). Linear regression analyses provided the following equations to represent the relationship between: bacteria and chlorophyll a (Chl a), log Bacteria = 0.413 log Chl a + 6.057 (P = 0.003); and between bacterial production (BP) and net primary production (NPP), log BP = 0.896 log NPP – 0.394 (P = 0.004), which fitted with published results well. Comparison of annual carbon fluxes confirmed the prevalence of net heterotrophy in these coastal waters, and together with the low correlation coefficients, suggested the role of allochthonous organic matter in supporting heterotrophic activity.