The phylogenetic relationships among members of the lower Diptera (formerly known as the suborder 'Nematocera') have remained ambiguous. Traditional hypotheses of the interrelationships between the earliest lineages of true flies have been based largely on morphological evidence. Recently collected molecular evidence (gene nucleotide sequence data) for the systematics of the lower Diptera is presented here. Chapter one presents the results of phylogenetic analyses implementing multiple nuclear markers, amplified from all major lineages of lower Diptera. One ribosomal gene (28S rDNA) and three nuclear protein-coding genes (CAD, TPI & PGD) were sequenced from 64 ingroup taxa. Results from both parsimony and model-based (Bayesian MCMC and maximum likelihood) analyses supported traditional and novel relationships. The small, enigmatic family, Deuterophlebiidae (mountain midges), was resolved as the sister group of all remaining fly families. A number of groups (traditionally referred to as infraorders) are resolved as monophyletic, including the Culicomorpha (including a novel superfamily Simulioidea = Thaumaleidae + Simuliidae), Tipulomorpha (Tipulidae sensu lato + Trichoceridae) and Bibionomorpha sensu lato. Support was found for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae) and Ptychopteromorpha (Ptychopteridae), while the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infraorder Bibionomorpha is sister to the higher flies (Brachycera). Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, while protein-coding genes performed variably at different levels. In addition to elucidating relationships, ages of major lower dipteran clades were inferred based on molecular divergence time estimates using relaxed clock Bayesian methods and fossil calibration points. Chapter two presents the phylogenetic relationships among higher-level taxa within the Diptera family Tipulidae sensu lato (crane flies) based on gene sequence data. Two nuclear genes were sampled (28S rDNA & CAD) for 45 ingroup taxa, representing 44 genera and subgenera of crane flies. In general, 28S supported various traditional relationships, whereas data from CAD were conflicting. Phylogenetic analyses showed support for several major clades, including the Pediciinae, Cyindrotominae, Tipulinae, and parts of Limoniinae. Molecular data did not support a monophyletic Limoniinae, thus rejecting a four-family concept for Tipulidae. The Pediciinae are strongly supported as the sister-group to all other Tipulidae. The tribes Chioneini and Limnophilini (Limoniinae) appear to be paraphyletic with respect to each other, while the Limoniini appear to be a well supported group (with or without Helius and Elephantomyia). Several genera were unable to be confidently placed in a phylogenetic context based on the molecular data sampled, including Atarba, Dactylolabis, Dicranoptycha and Epiphragma.