The seas of Southern Java are located at the eastern equatorial Indian Ocean and therefore, they are strongly influenced by the Indian Ocean Dipole (IOD). Strong negative IOD occurred in 2016. However, none of the previous studies investigated its effect on the seas of Southern Java. This study aims to reveal the influence of the strong negative IOD in 2016 on the upwelling intensity along the seas of Southern Java as represented by surface temperature and chlorophyll-a. This research was conducted using satellite-based data and the analysis was based on climatology, anomaly and correlation for 15 years (2007-2021). The data used includes sea surface temperature (OISST), wind (ASCAT), IOD index (DMI), chlorophyll-a (OC-CCI), and sea level anomaly (altimetry). The findings show that the strong negative IOD in 2016 had a significant impact on sea surface temperatures which made these waters warmer. The most visible impact is through the sea surface temperature anomaly map where in 2016 throughout the year it experienced a positive anomaly with a value of 2°C higher than the climatological average. The value of chlorophyll-a in these waters has also dropped drastically which, when viewed from the anomaly map, has a value of 0.2 mg/m³ lower than the climatological average, especially during the upwelling month. This means that, strong negative IOD in 2016 reduced the upwelling intensity along the seas of Southern Java. We also found the propagation of downwelling Kelvin waves from the Indian Ocean to the Southern Java waters which bring warm temperatures and cause downwelling events during the strong negative IOD in 2016 that hampers coastal upwelling along the seas of Southern Java.