In the first chapter, I introduce the study organisms, non-biting midges in the genus Axarus. These are large flies that spend the majority of their lifespan living aquatically in submerged clays and rotting wood in the Connecticut River. The adult lifespan is very brief, on the order of three days, while the larvae live for one year. There are two species so far discovered in the Connecticut River, both new to science, and very closely related to each other. Both species coexist in distinct populations separated by areas where there is no suitable habitat for them; the primary habitat being clay that was deposited during the existence of glacial Lakes Hitchcock and Coös, with a secondary use of rotting wood also evident. The population genetic evidence indicates that wood is only inhabited near clay deposits though, and there is genetic separation between the populations, a fact that is established in Chapter 3. Chapter 1 provides the foundational biological information necessary to use these species in a study of population genetics. In the second chapter I show that populations of one of the species, herein referred to as A. species varvestris, is polymorphic for 4 chromosomal inversions, and that natural selection is acting on one of these inversions. The inversion in question results in a significant decrease in larval size when heterozygous, and increases in frequency within one generation. This is evidence of natural selection, and size-selective predation is suggested as a mechanism for the selection. An association between this inversion and the sex determination of the species is also shown. The third chapter presents a large dataset of chromosomal mutation frequencies that establishes marked cytogenetic differentiation between the populations of Axarus species varvestris. I suggest that this differentiation has occurred within a very short time-frame, on the order of 10,000 generations, and that the structure of the population cytogenetic relationships may reveal and be correlated with the ancient separation between the post-Pleistocene lakes that were present in the river valley following the last ice age. (Abstract shortened by UMI.)