The study carried out systemic geochemical analysis of the Lower Miocene oil and gas samples from the well Naga Utara-1 (NU-1) in the Kutei Basin, Kalimantan Island. The result shows that hydrocarbon source rocks of natural gas samples are sapropelic and deposited in weak reduction marine environment, with the source material dominated by aquatic organism and calculated Ro of about 1.2%, suggesting the mature source rocks for gas generation. However, hydrocarbon source rocks of the oil samples are humic and should be developed in weak oxidized terrestrial environment, with the source material dominated by terrestrial plants and the calculated Roabout 0.7%, indicating immature to early mature source rock for oil generation. Therefore, the source rocks for gas and oil should be in two different intervals: one is marine source rock with higher maturity, while the other is terrestrial source rock with lower maturity. Two sets of strata identified in the Kutei basin have some similarities as that hosting rocks suggested by the oil samples, but completely different from that indicated by the gas samples. The gas should be sourced from deep lower Miocene marine strata or even deeper such as Oligocene to Eocene lacustrine strata. The gas generated in deep marine or lacustrine strata migrated up along the faults, and formed high pressure entrapment within sandstone at the top of anticline, which was sealed by overlying limestone and shale layers. The discovery of marine source rocks indicates that the Lower Miocene marine strata or deep hydrocarbon source rocks in the Oligocene and Eocene lacustrine strata are favorable exploration intervals. The next work should shift exploration direction, with exploration objective layers focusing on Middle or Lower Miocene marine accumulation system, even deep Oligocene or Eocene petroleum plays.