Marine eels that live on the continental shelf, slope and deep-sea and in the pelagic realms of the ocean are distributed worldwide at tropical and subtropical latitudes, but little information is available about their biodiversity and ecology in most areas. Collections of their leptocephalus larvae that all live together in the upper few hundred meters of the ocean are one way to learn about the distributions, reproductive ecology, and life histories of these difficult to observe fishes. This study evaluated the biodiversity and spatial distributions of leptocephali collected during two surveys conducted to the west of the shallow banks of the Mascarene Plateau in the southwestern Indian Ocean. 1140 leptocephali of at least 94 species of ⩾14 families of anguilliform and notacanthid fishes were collected in Nov.–Dec. 2006 and Jan.–Feb. 2010 in overlapping areas west of the plateau. In 2006, 565 leptocephali of at least 71 species were collected at 42 stations in two transects from 8 to 18°S, with larvae of shallow-water eel species of the Congridae, Muraenidae, Ophichthidae and Chlopsidae being most abundant at the northern stations in warmer water to the west of the Mascarene Plateau. Some small leptocephali of those eel families appeared to be transported offshore by currents from areas including the Seychelles, but the distribution of the leptocephali of mesopelagic eels of the Nemichthyidae and Serrivomeridae were more widespread. In 2010, 575 leptocephali of at least 53 species were collected in a dense grid of stations with the smallest larvae of the Muraenidae and Ophichthidae being near the banks, and spawning occurring at the Cargados Carajos Bank. Small larvae of Conger collected in the southwestern edge of the grid indicated offshore spawning, which is similar to Conger species in the Atlantic and Pacific. Seasonal and geographic differences in the characteristics or compositions of leptocephali were apparent, with higher proportions of small larvae in 2010 than in 2006, but cluster analysis of assemblage structure found similar geographic structure between the two surveys. Thalassenchelys larvae were only collected in the same southern area in both surveys and nettastomatid and notacanthid larvae were only collected in the north in 2006. The two surveys suggested that there is a relatively high biodiversity of eels in the Mascarene Plateau area compared to some regions and that colder water temperatures may inhibit spawning of eels on the southern banks. The two types of sampling strategies (transects or grid survey) each had different advantages, which can be considered for use in future oceanographic surveys for leptocephali in other regions of the world.