Sub-Bottom Profiling (SBP) records and results of geochemical analysis of 12 surficial sediment cores from various water depths collected from the offshore Waropen Basin-Papua are presented. Presence of gas is clearly observed on sub-bottom profiler records. Shallow gas was identified through acoustic response due to gas accumulation and gas escape on sub-bottom profiles. Acoustic evidences of gas accumulations within near surface geology consist of high amplitude reflections and associated acoustic blanking, gas plumes and morphological features like pockmarks. Total organic carbon analysis of 12 surface sediment cores varies between 0.5% to 1.3% which indicate that the sediments have an abundance of organic matters. Gas chromatographic analysis of hydrocarbon composition detected only methane, a biogenic origin of shallow gas. Acoustic and geochemical evidence in the Waropen Basin indicates extensive shallow gas accumulations in the Late Quaternary sediments, some trapped within these deposits and some escape from seabed into the water column which then created a high distribution of pockmarks.