Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We sequenced seven plastid regions and the nuclear ITS1 - ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Key results: Topologies recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recover six monophyletic groups that we circumscribe into three subgenera and six sections. Putative fungal mimic characters serve as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, is recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Conclusions: Our analyses do not unambiguously support a single origin for all fungal mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction.