Most of polypeptides containing α,β-dehydroamino acids have important biological activity, so exploration of synthetic method has practical significance. In this paper, dipeptides were prepared from l-threonine by protecting of c-terminal allyl acetate, and condensing reaction with a series of N-Boc amino acid. Then, treatment of dipeptides obtained with DMAP, (Boc)2O and tetramethylguanidine in the acetonitrile occured β-elimination reaction to yield stereoselectively dehydrodipeptides. Structures of dehydrodipeptides were confirmed by 1H NMR, 13C NMR and MS. Analysis of 1H NMR, 2D NMR and crystal structure showed that the dehydrodipeptides were Z-configuration.Graphical abstractDehydrodipeptides were prepared from l-threonine. Their structures were confirmed by 1H NMR, 13C NMR and MSElectronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-2005-z) contains supplementary material, which is available to authorized users.