The jumping organ (furcula) is the most characteristic structure among collembolans, and it is of great taxonomical values at higher levels. The largest superfamily Entomobryoidea is traditionally classified into four families only by the morphology of the furcula. Actually, many taxa among these families are strikingly similar in morphology without considering furcula. The phylogeny of Entomobryoidea was reconstructed here based on mitochondrial and ribosomal fragments. This indicated that both Paronellidae and Cyphoderidae were ingroups within Entomobryidae with the former polyphyletic. Topology tests, which used the likelihood and Bayesian approaches, also rejected the traditional hypotheses relying on furcula morphology. Further ancestral state reconstructions have revealed that traditional taxonomical characters, i.e., furcula and body scales, had multiple independent origins in Entomobryoidea whereas tergal specialized chaetae (S-chaetae) exhibited strong phylogenetic signals. By integrating both molecular and morphological evidence, the results of this study drastically undermine the present classification of Entomobryoidea. Tergal S-chaetotaxic pattern in combination with other characters are more reasonable in taxonomy at suprageneric levels than convergent furcula. This study provides new insights of the jumping organ, which could be adaptively modified during evolution of Collembola.