Phytophthora is a genus comprising upwards of 100 species. The most recent phylogeny of the genus was inferred from seven nuclear genes (Blair et al., 2008) and was subdivided into 10 well-defined clades that are concordant with the morphology-based Waterhouse criteria (Waterhouse, 1963; Kroon, 2010). The description of new species in this genus has traditionally been based on morphological characters, ecology, geography and host specialization. Although these traits are useful in the nomenclatural recognition of different species, they are not necessarily correlated to their evolutionary history and thus should not be used alone as characters to define new species. It is now routine that new Phytophthora species descriptions also include a detailed phylogenetic analysis typically based on several loci. In an evolutionary context, reproductive isolation of a species from other close relatives is a fundamental requirement of the biological species concept (Mayr, 1942). The use of molecular markers, traditionally the nuclear internal transcribed spacer (ITS) region, has allowed recognition of species complexes such as P. citricola and P. megasperma. In species complexes the definition of species boundaries is difficult. When is a species in a lineage differentiated enough to be considered as a separate one (Mishler, 1985; Avise & Ball, 1990)? We believe that careful analysis of several nuclear and mitochondrial loci is needed to support the definition of species boundaries. Here we examine problems of defining species boundaries using the example of the recently proposed new species, Phytophthora andina.