The potential fishing zones detected by remote sensing satellite data in this study focused on the key region of small pelagic fish in the Makassar Strait in the Java Sea, Indonesia. The remote sensing satellite data used sea surface temperature (SST) and chlorophyll-a (Chl-a) imagery obtained from the Aqua-MODIS Level 3, with a time coverage of more than ten years. The fishing production data were sourced from fish landing records in the Nusantara Fishing Port of Pekalongan (PPN Pekalongan), Central Java, Indonesia. The mapping overlay method and cross-correlation analysis were used to determine the variability of relationships between sea surface temperature and chlorophyll-a and small pelagic fish catches. The pattern of fishing migration areas showed that spotted sardinella was dominant in the northwestern monsoon period, with the direction of movement towards the north of Makassar Strait controlled by warm SST. However, the shortfin scad was dominant in the southeast monsoon period with movement towards the south of Makassar Strait up to the east of Java Sea which is controlled by high Chl-a. The increase of shortfin scad catches occurred after 4 months of maximum Chl-a achievement, while spotted sardinella increased in 3 months before the maximum Chl-a achievement. For the SST, these two types of fish respond directly to changes in the waters. To the El Nino event, fish catches experienced an increase that was dominated by shortfin scad; while during La Nina, fish catches that experienced a decrease were dominated by spotted sardinella.