The Triodopsis genus of Stylommatophoran land snails has been confusing to malacologists for decades. Twenty-eight species have been described in the eastern and southern US, but some original descriptions are insufficient to correctly identify specimens, and misidentifications are common. Phylogenetic approaches have not been applied for species in this genus as the usual mitochondrial markers are extremely variable and difficult to sequence. DNA extraction is complicated by the presence of mucopolysaccharides. A mollusk-specific DNA extraction protocol and custom primers are developed in this study to better facilitate genetic analysis of the family Polygyridae. Triodopsis genus phylogenies based on 16S, ITS2, and H3 genes are presented, with FST values suggesting a reduction in the number of named species. The phylogenetic clades are related to morphology and biogeography to attempt to better identify the recognized species and change the species status of some based on morphology measurements and overlapping distributions. An H3 molecular clock tree suggests a recent and rapid expansion in the family. New hypotheses are also presented that may explain the genetic variation in the Stylommatophoran mitochondrial genome, and a possible explanation of the morphological variation within a clade that could still be undergoing rapid speciation after repeated refugia isolation.