© 2018 Elsevier Ltd The unique semi-enclosed Indian Ocean basin includes large Mascarene Plateau banks, offshore coral-reef islands, seasonal equatorial current jets, and cross-basin westward South Equatorial Current (SEC) flow, making it interesting for studying long larval-duration eel larvae (leptocephali) and regional eel biodiversity. Three surveys for leptocephali (in 2003, 2006, 2010) included sampling west of the Mascarene Plateau (west), a major survey and other stations off Sumatra and Java (east), and 2 cross-basin transects across the SEC. The highest numbers of leptocephali species were observed along Sumatra (2003: ~143 species; 2006: 72 species) and south of Java (2010: 69), with intermediate numbers being collected in the western Indian Ocean (2006: 71; 2010: 53) compared to low numbers in the hydrographically variable offshore zones (2006, 2010: 3–27). The larger continental shelf areas along Sumatra including the Mentawai Islands provide more coral reef and other habitats for species such as congrid, muraenid, ophichthid, and chlopsid eels compared to the Mascarene Plateau banks. Some larvae in these areas get transported offshore, but the majority of offshore larvae were of Nemichthyidae and Serrivomeridae mesopelagic eels that were spawning across the basin. Habitat differences between the southern Mascarene Plateau and Sumatra and southern Indonesia along the edge of the high biodiversity Coral Triangle likely explain the higher biodiversity of eel larvae observed along the western side of the basin, which for the Congridae and Ophichthidae included more species than observed previously within the central Indonesian Seas. In addition to local spawning, seasonal currents likely transport larger larvae towards Sumatra from the north or west and larvae may enter the basin from the Indonesian Throughflow in the east, but it is unknown if equatorial jets or the SEC can transport larvae across the whole basin.