The cyprinid subfamily Danioninae is one of the most important fish groups due to its inclusion of the model fish, Danio rerio. Molecular investigations have shown that species traditionally placed in the Danioninae are non-monophyletic, divided into two groups corresponding to the Danioninae and Opsariichthyinae. The Danioninae are further divided into three lineages, i.e. chedrins, danionins and rasborins. However, morphological characters determining the foregoing groups are unknown. To investigate the interrelationships among major lineages within the Danioninae, a phylogenetic analysis based on 43 morphological characters from 34 taxa was conducted. Parsimony analysis recovers the Danioninae and Opsariichthyinae to be distinguished by the Y-shaped ligament, absent in the Danioninae while present in the Opsariichthyinae. The Danioninae are divided into two tribes, Danionini and Rasborini. The Rasborini, including Boraras, Brevibora, Horadandia, Kottelatia, Rasbora, Rasboroides, Rasbosoma, Trigonopoma and Trigonostigma, are diagnosed by presence of dark supra-anal pigment and subpeduncular streak as well as presence of the rasborin process on epibranchial 4. The Danionini are composed of two subtribes, Danionina and Chedrina, the Danionina including Chela, Danio, Devario, Microdevario and Microrasbora, and the Chedrina comprising Chelaethiops, Esomus, Luciosoma, Megarasbora, Mesobola, Nematabramis, Opsarius, Raiamas and Salmophasia. The Danionina are diagnosed by the unossified interhyal and presence of the danionin foramen in the horizontal limb of the cleithrum while the Chedrina are characterized by the postcleithrum absent or greatly reduced and approximately normal to abdominal ribs when present.