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With 36 species and at least nine potentially independent lineages (not formally described yet) occurring mostly in the Andes and adjacent Patagonia and Puna plateau areas, Phymaturus lizards represent one of the most endemic vertebrate groups of the arid southwestern region of South America. Phylogenetic relationships among species of Phymaturus are inferred using mainly a morphological data set of 206 characters. Also available sequences of mitochondrial DNA for seven terminals were added for a total evidence analysis. Most information is included in the discrete characters block; most characters involve color pattern, osteology and squamation. Continuous characters were taken from body proportions, squamation and skeletons. Among morphological data, binary polymorphic characters were analyzed applying the scaled coding criteria. Continuous characters were entered in the analysis using standardized ranges, a method that allows a simple optimization to estimate distances/costs avoiding the arbitrary coding as discrete characters. For our parsimony analyses we chose the implied weights method, which underweights homoplastic characters. Several runs were made analyzing all the information combined and also separating morphological from molecular datasets. Binary polymorphisms were also analyzed as missing data. All characters affected by sexual dimorphism were analyzed separating the sexes; female information was more congruent with the total evidence analysis. Characters involving continuous and polymorphic information are relevant for searching and building phylogenetic hypotheses in Phymaturus. There exists significant congruence between the molecular information analyzed in this study and previous published analyses. Within both main clades of Phymaturus, northern subgroups are those more recently originated during the genus diversification. Species belonging to the puna subclade of the palluma group are arranged in two natural groups, one distributed in the north (Catamarca and La Rioja provinces), and the other in the south, La Rioja and San Juan provinces. Within the patagonicus group, the majority of the species are arranged in a south-central Chubut clade, eastern-central Chubut clade, central Rio Negro clade and a Payunia clade.