Using remote sensing of sea surface temperature (SST), sea surface height anomaly (SSHA) and chlorophyll-a (Chl-a) together with catch data, we investigated the detection and persistence of important pelagic habitat hotspots for skipjack tuna in the Gulf of Bone-Flores Sea, Indonesia. We analyzed the data for the period between the northwest and southeast monsoon 2007–2011. A pelagic hotspot index was constructed from a model of multi-spectrum satellite-based oceanographic data in relation to skipjack fishing performance. Results showed that skipjack catch per unit efforts (CPUEs) increased significantly in areas of highest pelagic hotspot indices. The distribution and dynamics of habitat hotspots were detected by the synoptic measurements of SST, SSHA and Chl-a ranging from 29.5° to 31.5°C, from 2.5 to 12.5 cm and from 0.15 to 0.35 mg m-3, respectively. Total area of hotspots consistently peaked in May. Validation of skipjack CPUE predicted by our model against observed data from 2012 was highly significant. The key pelagic habitat corresponded with the Chl-a front, which could be related to the areas of relatively high prey abundance (enhanced feeding opportunity) for skipjack. We found that the area and persistence of the potential skipjack habitat hotspots for the 5 years were clearly identified by the 0.2 mg m-3 Chl-a isopleth, suggesting that the Chl-a front provides a key oceanographic indicator for global understanding on skipjack tuna habitat hotspots in the western tropical Pacific Ocean, especially within Coral Triangle tuna.

The Java Sea with a surface area about 467.000 km2, is located in the South East Sunda Shelf with the average of depth is 40 meters, affected by several phenomena, whether physical or meteorological. This research aims to analyze the characteristics of water masses in the Java Sea and its relationship with the periodicity of the monsoon and Indonesian Throughflow Water (ITF) phenomenon. Then analyze the exchange of water masses in the Java Sea. The data used are temperature and salinity to identify the characteristics of the water masses. Ocean currents data to identify ITF patterns and winds data to identify the monsoon patterns. The data used in 2015 from the Infrastructure Development of Space Oceanography (INDESO) sites with a resolution of 1/12°. The method used is a descriptive analysis of spatially and temporally. The results show that averaging seasonal found that southeast monsoon period salinity is higher (31-34 psu) than northwest monsoon period (29.5-33 psu), and southeast monsoon period temperature is lower (27-30.5°C) than northwest monsoon period (28.5-30.5°C). ITF phenomenon occurs in May through September and reaches its peak in June, July, and August. ITF strengthened in southeast monsoon and weakened in the northwest monsoon. ITF and monsoon have similar impacts on salinity and temperature in the Java Sea. The water masses in the Java Sea comes from the South China Sea and Makassar Strait. In the northwest monsoon, Java Sea filled by water masses of the South China Sea, while in the southeast monsoon phenomenon which coincides with ITF phenomenon, Java Sea water masses is filled by water masses from Makassar Strait. In the transition monsoon I and II, the Java Sea filled by the South China Sea and the Makassar Strait water masses.

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