Volatile organic compounds (VOCs) affect oxidant loadings and secondary organic aerosol formation in the lower atmosphere. The marine environment is thought to be an important global source of biogenic VOCs (BVOCs). This paper presents sea-to-air fluxes and spatial and temporal distributions of the BVOCs, isoprene and monoterpenes, in the coastal upwelling region off the east coast of the Malaysian Peninsula. The overall fluxes ranged between 10⁷ and 10⁸ molecules/cm²/s, which is comparable with open ocean values. Isoprene dominated the overall fluxes with an average percentage of 65% compared to monoterpenes (total) (35%). Among the monoterpene compounds, β-pinene showed the highest average flux, followed by α-pinene and limonene. The spatial distribution suggests that isoprene fluxes potentially correspond to the sea surface water nutrients compared to monoterpenes. There was a significant relationship between isoprene and monoterpene (total) fluxes (R = 0.73, p < 0.01), which could indicate that both isoprene and monoterpene are controlled by the same biological factor (e.g., chlorophyll-a). According to the findings of this study, the upwelling region off the east coast of the Malaysian Peninsula could be a significant source of atmospheric isoprene and monoterpenes.