Genetic conflict occurs when one portion of the genome promotes its owntransmission at the expense of another portion. Genetic conflict is ubiquitous, and canhave significant evolutionary consequences. Meiotic drive is a kind of genetic conflictthat occurs when one allele manipulates normal processes during meiosis orgametogenesis to be overrepresented in the gametes. X-chromosomes carrying meioticdrivers are known as sex-ratio X-chromosomes (SR) because they manipulatespermatogenesis to sabotage the production of Y-bearing sperm, resulting in the carriermale siring only daughters. The North American fruit fly Drosophila neotestacea harborsan SR system found at steady frequencies of up to 30% in some populations. In thissystem, there are no known suppressors or drive and 99% of offspring produced by SRmales are daughters. In this dissertation, I investigate the molecular evolutionaryconsequences of drive in this system and identify candidate genes for the molecularmechanism. I show that SR carries large inversions and is significantly geneticallydifferentiated from the standard X-chromosome (ST), but there is evidence that gene flowoccurs between ST and SR. I find variation on SR is not present in distinct haplotypes,but is likely maintained through recombination in SR homozygous females. I thenidentified hundreds of transcripts that are differentially expressed between ST and SR inthe testes. Most of these transcripts are located on the X-chromosome, and differentialexpression begins early in spermatogenesis. I also found dozens of transcripts that showpatterns of nucleotide sequence differences between ST and SR that are suggestive ofpositive selection. I identified candidates for the mechanism of drive as differentiallyexpressed, testis-specific transcripts under putative positive selection. One of thesecandidates is a fast-evolving X-linked duplicate of the autosomal gene importin-a2, acritical part of the nuclear import pathway. At this locus and other candidates, I foundmolecular population genetic patterns consistent with involvement in the mechanism ofdrive: relaxed purifying selection in ST and positive selection in SR. Nuclear import isalso targeted by a meiotic driver in D. melanogaster, suggesting that this process may beparticularly susceptible to conflict.