The genera Butea, Meizotropis and Spatholobus (Leguminosae—Papilionoideae), occurring in continental Southeast Asia and the West Malesian Archipelago, are treated phylogenetically with Kunstleria as an outgroup. The genera Spatholobus (29 species), Butea and Meizotropis (each 2 species) are usually placed in the tribe Phaseoleae of the Papilionoideae, whereas Kunstleria belongs to the less advanced tribe Millettieae. Spatholobus is probably basal in the Phaseoleae. An analysis with PAUP of the datamatrix containing 80 macromorphological, 10 leaf anatomical and 7 pollen morphological characters resulted in three most parsimonious trees (MPTs) with a length of 589 steps. As for the method, it turned out that the option ‘addition sequence random’ gave more MPTs than an ‘addition sequence simple’. The standard option ‘addition sequence simple’ with taxon one as reference taxon resulted in trees a few steps longer than the MPTs. One of the three phylogenetic trees has been chosen to be used for the biogeographic analysis. Other genera used for this analysis are Fordia (Leguminosae—Papilionoideae), Genianthus (Asclepiadaceae), and Xanthophytum (Rubiaceae). Within Southeast Asia 29 areas of distribution were recognised. Although they are solely based on the distribution pattern of the species, some areas coincide with geological entities, e.g., E Malaya and SE Sumatra. The biogeographical analysis performed by PAUP (BPA) and CAFCA (CCA) resulted for PAUP in 19 MPTs under assumption 0 with a length of 366 steps and 324 MPTs under assumption 1 with a length of 316 steps; for CAFCA the analysis resulted in 1 MPT (450 steps) under assumption 0 and 1 MPT (417 steps) under assumption 1. In all results more or less the same larger groups of areas were present: the areas recognised on Borneo, those on the Malay Peninsula together with SE Sumatra and W Java, and the areas on the continent of Southeast Asia. Some areas with only one species were found basal to the other nodes, and were considered not informative. After comparing the 19 MPTs, the 50% Majority-rule consensus tree was used to discuss the possible link with the geology. The geology of the region is very complex as there are four major tectonic plates in collision with each other: the Eurasian Plate, the Indo-Australian Plate, the Pacific Plate, and the Philippines Sea Plate. A summary of the geology of Southeast Asia is given. It is probable that the general area-cladogram reflects the split (during high sea level) between continental Southeast Asia and Peninsular Malaysia and the Malay Archipelago. Furthermore it is remarkable that the areas in Borneo are splitting off in the order of age, where the youngest areas are at the top and the oldest at the base of the tree. The history of the genus Spatholobus is hypothesised by backtracking the phylogenetic relationships on the general area-cladogram. Probably the history of Spatholobus was influenced by the differences in sea level. During low sea levels the Sundaland Plateau was dry and it was possible to migrate into the Malesian Archipelago, but high sea levels resulted in isolation and speciation. It is impossible to say more about timing than that it could have started at the earliest in the Early Eocene. In the last case the ancestor of the genus was present in an area without the northern parts of Borneo, and with the south arm of Sulawesi still connected to Borneo.