The Bay of Bengal (BOB) is a semi-enclosed marginal sea in the northeastern part of the Indian Ocean. The South China Sea (SCS) is almost an enclosed marginal sea and is part of the northwestern Pacific Ocean. Both of them are tropical marginal seas, and have similar hydrological properties, such as high surface temperature, stable thermocline, deep euphotic zone, etc. Moreover, they are all greatly affected by East Asian monsoon and typhoons. However, there are also several significant differences between them. The current circulation structures in the South China Sea are more complex with significant season variations. A large amount of fresh water through river inputs is one of the remarkable hydrological characteristics in the Bay of Bengal. In addition, the Bay of Bengal has a large volume of precipitation. Therefore, it is naturally interesting to investigate the different response of the marine ecological properties represented by chlorophyll concentration to climate change. The Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) mission have provided a successive, long-term observations of global ocean color from space. In this study, we investigate the Chl-a trends in the BOB and SCS during the SeaWiFS and MODIS observation periods (1998-2010 and 2003-2016), respectively. In 1998-2010, Chl-a increased in the western central basin of BOB, while it decreased in almost all other parts. During 2003-2016, Chl-a significantly increased in the western part of BOB, and reduced in the southern part. In the SCS, Chl-a in almost the whole region increased during the SeaWiFS observation period. In 2003-2016, the major rising trends appeared in China and Vietnam coast, the Beibu Gulf, and the Gulf of Thailand. The Chl-a of the Straits of Malacca and the Karimata Straits showed downward trends. The rise in temperature might be the main cause of the Chl-a decrease in the BOB. The deepened MLD and/or decreasing SST may contribute to the increasing Chl-a of the BOB and SCS. Remarkably, coastal Chl-a has continued to rise over the past 19 years. The freshwater input might have significant effect on it.