Many areas of systematic ichthyological research remain wide open for investigation in the Indo-Pacific. Undescribed species and other valuable material are expected from relatively unexplored marine and freshwater habitats and regions. For example, from the marine realm deep reef, outer shelf, and deep sea habitats have been sparsely collected with mostly inadequate gear. Many lakes and rivers in the region have never been visited by an ichthyologist. Certain areas such as Sumatra, where rich freshwater fish faunas are expected, require extensive additional collections. The freshwater fish fauna of Myanmar needs serious critical review. In addition to habitats and regions, certain groups of fishes from the region remain highly problematic taxonomically. For example, most marine anguilliform and many cypriniform groups require extensive revisionary work. The complex and often unresolved geological history of the region, particularly around Southeast Asia continues to confound both marine and freshwater biogeographic hypotheses. Only a handful of phylogenetic hypotheses down to species level are available among the numerous fish families, leaving biogeographic models largely untested and supraspecific classification less defensible. New collecting and analytical methods, infusions of scientific support, and plenty of dedicated research time are required to make significant research achievements. Many of these research gains are urgent, in view of the increasing degradation of both marine and freshwater habitats of the Indo-Pacific.