Mesophotic coral ecosystems (MCEs) are characterized by light-dependent corals and associated with communities typically found at depths ranging from 30~40 m to over 150 m in tropical and subtropical regions. MCEs represent approximately 80% of potential coral reef habitat worldwide, yet very little is known about them in comparison with shallow reefs. In the previous studies, we explored the possible hot spots of the mesophotic coral across the southern of Taiwan, Xiao Liuqiu, Hengchun Peninsula and Lanyu island. The diversity and abundance of coral at Lanyu island is the highest. At the west part of Lanyu island the scleractinian can be found at depth around 75m, moreover, other Hexacorallia, such as Antipatharia, and Stylasteridae can be found from 40m to 150m. Among the three places we surveyed, Lanyu island at 50m has the best light penetration rate (more than 40%) and the light spectrum is wider than Xiao Liuqiu, Hengchun Peninsula. The distribution of Scleractinian at different depth is correlated to the benthic substrate and light penetration rate. Light penetration rate is affected by suspended solids including plankton and the nutrients which are influenced by currents, temperature, salinity and terrigenous materials. In the present study, we use underwater remotely operated vehicle (ROV) to explore the mesophtic coral at Southern Taiwan. The preliminary data showed that here in southern Taiwan, while most coral are Nephtheidae, Ellisellidae and Nidaliidae, there are a few Scleractinia (such as Fungiidae or Agariciidae) at upper MCEs zone. At lower MCEs zone, the majority were Octocorallia, Nephtheidae, Ellisellidae, Nidaliidae, Plexauridae, and some Hexacorallia (such as Antipatharia and Dendrophylliidae). According to the lipid analysis, samples collected from mesophotic region generally had lower lipid content, and specifically the contents of neutral lipids, triacylglycerol, and polar lipids (free fatty acid) in MCEs were lower than those in shallow water. Furthermore, the ratio of poly-unsaturated fatty acids was higher in samples collected from mesophotic zone than from the shallow water. These results indicate that Scleractinia in MCEs is heterotrophic instead of autotrophic.