Here we describe two new species of genus Piper L. from Madagascar: Piper malgassicum and Piper tsarasotrae, the species names referring to the currently known distribution areas. These two species contribute, at least in part, to the production of local voatsiperifery pepper, probably mixed together with P. borbonense, and are therefore economically relevant as spices. We used a selected set of characters (those more easily observable on herbarium samples) for principal component analysis to assess the relative distance between the species, including the analysis of the autochthonous species of Piper known from Africa and Madagascar. In order to check the identity and assess the phylogenetic position of the two species, we also sequenced the chloroplast gene ndhF, the trnL intron, and the nuclear gene G3pdh. On the basis of these results we show here the relationships between these two new Piper taxa and the most closely related species within the genus (excluding P. heimii and P. pachyphyllum, for which only morphological characters were available).