Two distinct CO2 sink/source characteristics appeared from the compiled observed data 1984-2013 in the tropical Indonesian seas. The western part persistently emits CO2 to the atmosphere, while the eastern is rather dynamic which emits and absorbs smaller amount of CO2 to and from atmosphere, respectively. The segregation is proximal to the virtual Wallace line, where in the continental shelf is located. Lower salinity and higher silicate condition in the western part influenced the higher pCO2 condition in Java Sea. Sea temperature is found to have a limited influence to control different characteristic in the west and east, but sea surface temperature (SST) change of 2.0 oC during La Ninã condition effectively reduced the source amount of CO2 by 50% compared to Normal year condition. Yet, during La Ninã, higher wind speed increases CO2 flux twice compared to Normal year. In the continental shelf area where CO2 sink area is found, 29 years data showed that pCO2 trend is increasing ±0.6-3.8 µatm/year. From this study, the overall areas have a significant source of CO2 of approximately 10 – 24 µatm.