Pedicularis L. (Orobanchaceae) is a large hemiparasitic genus, distributed mostly over boreal and arctic-alpine regions of the northern hemisphere. In the present study 9 species of the genus that are reported in flora of Iran, were undertaken for stigma morphological study and numerical analysis. The stigmatic surface is even in P. pycnantha and P. wilhelmsiana, is expanded into a subspherical shape in P. cabulica, P. caucasica, P. rechingeri, P. sibthorpii, P. condensata and P. strausii and is conical form in P. rhinanthoides. To determine the relationship between species, numerical analysis was carried out using 45 quantitative and qualitative morphological, anatomical and palynological characters. UPGMA and PCA dendrograms were drawn. According to the results some characters such as the thickness of  pericarp, the thickness of  spongy parenchyma, the length of  stem, the thickness of bark, the thickness of  stem and the length of midrib are the most variable, and can be used for identification and determination of relationship between species.