Addressing the taxonomy of morphologically complex groups can be challenging. Correlating results from multivariate morphological analyses and molecular data and reconciling these with geographic distributions allowed us to address the classification of the taxonomically difficult Taxus wallichiana complex in China and surrounding areas. We used 27 morphological characters (phenotype) and sequences of the chloroplast trnL-F intron/spacer region (genotype) on 1240 samples of 79 populations and 43 type and paratype specimens and demonstrated a strong correlation between phenotype and genotype and geographic distribution. We were able to define the number of taxonomically discrete units in the complex and delineate the geographic distribution of five species, T chinensis, T florinii, T mairei, T wallichiana and the here described new species T calcicola in China and adjacent regions. These are much fewer than the number of recently proposed species and these exhibit greatly non-overlapping and continuous distributions. Based on descriptions of species-"typical" specimens, we prepared species-specific morphometric profiles, that allowed the generation of a species differentiation matrix, allowing the quick selection of the most suitable characters for the separation of any species pair. This work represents a step forward towards the completion of a workable taxonomy of Asian Taxus.