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.

Remotely derived environmental variables, including sea surface height anomaly (SSHA), sea surface temperature (SST), chlorophyll-a (chl-a), eddy kinetic energy (EKE), mixed layer data set of argo float (MLD), Niño 3.4 index, and bigeye tuna catch data for the period 1997–2008, were used to analyse ocean climate variability and how they relate to the hotspots of bigeye tuna catch in the eastern Indian Ocean off Java. The empirical orthogonal function (EOF) was performed to obtain a more detailed structure of the spatio-temporal ocean variability in the region. The results showed that the first EOF modes of chl-a, SSHA, and SST accounted for 42.8%, 36.5%, and 27.4% of total variance, respectively, and these corresponded to the interannual signal. The maps of spatial patterns of the first EOF modes of SSHA, SST, and chl-a gave very typical values for cold-water SSHA, low SST, and high chl-a concentration along the southern coast of the Indonesian archipelago; and warm-water SSHA, high SST, and low chl-a concentration in the offshore region to make frontal areas along the latitudinal line around 10–12º S. The EOF analysis further revealed a strong relationship between the El Niño event and favourable oceanographic conditions, resulting in a significant increase in bigeye tuna catch. The average hook rate of 0.71 (0.43) was recorded during El Niño (La Niña). Major hotspots were located away from the confluence region and frontal areas around 11–16° S and 110–118° E and were thus demonstrated as the most favourable oceanographic conditions for bigeye tuna fishing in the eastern Indian Ocean off Java.