The highest biodiversity of marine fishes occurs in South-east Asia in the Indo-Australian Archipelago (IAA). However, the fossil record of fishes is very sparse and extremely incomplete in the IAA. Here we present a diverse fossil cartilaginous fish fauna from Borneo, found in late Miocene sediments in Brunei Darussalam. This fauna provides the first insight into the types of fishes that existed in the IAA region about 6.5–8 million years ago. The chondrichthyan remains belong to 24 selachian and batoid taxa. The shark fauna is dominated by Carcharhiniformes, comprising three families with at least 12 taxa, most related to modern species: Hemigaleidae (one species), Carcharhinidae (nine) and Sphyrnidae (two). In addition, the teeth of one Lamniformes shark, the extinct giant macro-predator Otodus (Megaselachus) megalodon, are present in the fauna. The batoids are dominated by Myliobatiformes from the following families: Dasyatidae (three species), Aetobatidae (one), Myliobatidae (three), Rhinopteridae (one), while three taxa of the order Rhinopristiformes were also recovered: Pristidae (one species), and Rhinidae (two). Such diversity of fossil cartilaginous fish has never before been reported from the tropical region of South-east Asia. The dominance of the carcharhinid sharks and small rays suggests a shallow marine, coastal palaeoenvironment. The presence of the freshwater shark genus Glyphis indicates a nearby fluvial influence. Some species of the ray genera, such as Himantura or Pastinachus, have also been reported from estuaries and fresh water. The lack of some generally common Neogene taxa, such as Odontaspididae, Lamnidae and Alopidae, may be linked to such local factors and the coastal shallow-water environment.