The phylogenetics of 40 taxa of European bumblebees were analysed based on PCR amplified and direct sequenced DNA from one region of the mitochondrial gene Cytochrome Oxidase I (1046 bp) and for 26 taxa from two regions in the nuclear gene Elongation Factor 1α (1056 bp). The sequences were aligned to the corresponding sequences in the honey bee. Phylogenetic analyses based on parsimony, as well as maximum likelihood, indicate that the bumblebees can be separated into several well-supported clades. Most of the terminal clades correspond very well with the clades known from former phylogenetic analyses based on morphology and recognized as the subgenera: Mendacibombus, Confusibombus, Psithyrus, Thoracobombus, Megabombus, Rhodobombus, Kallobombus, Alpinobombus, Subterraneobombus, Alpigenobombus, Pyrobombus, Bombus and Melanobombus. All the cuckoo bumblebees form a well-supported clade, the subgenus Psithyrus, within the true bumblebees. All the analyses place Kallobombus as the most basal taxon in contradiction to former analyses. The other deeper nodes of the phylogenetic trees, which are weakly supported, deviate significantly from former published trees - especially the trees based on mtCO-I. Presumably, the reasons are that multiple hits and the strong bias of the bases A and T blur the relationships in the deepest part of the trees. Analyses of the region in mtCO-I show a very strong A+T bias (A+T= 75%), which also indicate preferences in the use of codons with A or T in third positions. In closely related entities, there is only a weak transversion bias (A+T). In the studied regions in EF 1-α, no nucleotide bias is observed. The observed differences in bases between the investigated taxa are relatively small and the gene is too conserved to solve all the questions that the analyses of the deeper nodes using mtCO-I raise.