A reinvestigation of type and other material of Baetisjavanicus Ulmer, 1913 and Baetissabahensis Müller-Liebenau, 1984, together with new material from Southeast Asia revealed a new genus, Branchiobaetis gen. nov. The above species are formally assigned to the new genus Branchiobaetis gen. nov. It is characterized by the presence of accessory gills ventrally near fore coxa and at the base of maxillae, a peculiar folding of the gonostyli developing under the cuticle of last instar male larvae, together with a unique combination of other larval characters. Besides the two formerly described species, five new species are identified using a combination of morphology and molecular characters (COI, Kimura 2-parameter distances), four species from Sumatra and one from the Philippines. They are described and illustrated at the larval stage. Additionally, a complementary description of larva and adult stages of the generic type species B.javanicus comb. nov. as well as the first description of the eggs are provided. Furthermore, new reports of B.javanicus comb. nov. and B.sabahensis comb. nov. are indicated. The distribution of Branchiobaetis gen. nov. includes the Indonesian Sunda Islands, Borneo, and the Philippines. A key to the larval stage of all species is provided.