High carbon dioxide in reservoirs limits successful exploration in many petroliferous basins, particularly in Southeast Asia. High reservoir CO2 in the offshore Malay Basin represents a significant exploration challenge. Some fields contain >80% CO2, which makes them unattractive targets for development. Various hypotheses on the origin of CO2 have been proposed but remain controversial. This paper shows that geochemistry and advanced petroleum system modeling help to resolve the origins of reservoir CO2 and allow quantitative estimates of CO2 in prospective reservoir targets prior to drilling. A novel workflow estimates the CO2 content in reservoirs based on knowledge of the chemical mechanisms for the origin of the CO2 and numerical simulation of geologic burial history. Heat flow, deposition of overburden rock, and the kinetics of specific reaction mechanisms control the timing of CO2 generation and the relative contributions of CO2 from different sources. In this study, stable carbon isotope ratios of CO2 and methane (δ13CCO2 and δ13CCH4, ‰) were used to identify the source of the CO2 in Malay Basin gas samples. For example, Figure 3 shows δ13CCO2 and δ13CCH4 for samples from various depths in the nearby field. The isotope data indicate that the samples contain mixed CO2 derived by different mechanisms from two sources. Partial least squares (PLS) regression of δ13CCO2 and δ13CCH4 and depth for 61 samples from the nearby field, where %CO2 was set as the dependent variable, resulted in a systematic correlation between predicted and measured %CO2. Alternate least squares (ALS) confirms that the data can be explained by mixing of gases from two endmembers: (1) shallower samples show lower %CO2 that is isotopically depleted in δ13CCH4 and δ13CCO2, and (2) deeper samples show higher %CO2 that is isotopically enriched in δ13CCH4 and δ13CCO2. The relative proportion of each endmember in the mixture can be calculated for each gas. Examples of near endmember gases in the nearby field (Figure 3) are: (1) shallow thermogenic CO2 derived by cracking of kerogen, e.g., 1681 m, 5% CO2, δ13CCH4 = -60‰, δ13CCO2 = -13‰, (100:0 mix); and (2) deep CO2 from carbonate decomposition, e.g., 2918 m, 74% CO2, δ13CCH4 = -32‰, δ13CCO2 = -3‰ (15:85 mix). These results are consistent with the general observation that tested Miocene traps in the Malay Basin and show a general trend of higher concentrations of CO2 in the deeper traps that are nearer carbonate basement. Biogenic CO2 may represent a third endmember in other parts of the basin.