Helitrons are a type of ancient mobile DNA in eukaryotes. Previous studies have shown that Helitrons are abundant within the maize genome, comprising more than 2.2% (over 50 Mb) of the total nuclear genome. Their presence throughout the tree of life suggests early evolutionary beginnings. Due to their ability to capture genomic DNA fragments and rearrange functional genic sequences, these transposable elements (TEs) have the potential for de novo gene creation.This dissertation gives insight into evolutionary dynamics of Helitrons in the maize genome. I identified, de novo, presence-absence variation of Helitrons in the fully sequenced genomes of 26 diverse maize inbreds. Each inbred in the population was predicted to have ~67,000-72,000 Helitrons by the software HelitronScanner, yet only about 25% (~17,000-18,000) of these were confirmed in my more detailed analysis. I randomly selected one Helitron from each of the ten chromosomes in the inbred B73 to serve as loci for comparison across the entire inbred data set. Genes flanking these ten Helitrons were analyzed to confirm Helitron orthology, to investigate the phylogenetic history of the genome segments containing these Helitron insertions, and to determine the rates and nature of sequence change. Neither the Helitrons nor the flanking genes across the ten loci yielded phylogenies that were identical to the overall phylogenies that relate these 26 inbreds, showing that segmental introduction from many (and often distantly related) maize genome resources were involved in the construction of these inbreds. Mutations were identified in Helitrons and in flanking gene coding regions, intronic regions, and within 500bp of the 3’ ends. Polymorphic insertion/deletion (indel) sizes and natures within Helitrons were rigorously described. Among identified indels, TE insertions were prominent. Phylogenetic analysis of these Helitrons allowed for determination of the direction of specific mutations (e.g., G to A versus A to G or insertion versus deletion), discovering that small deletions were particularly common and that C/G to T/A transitions were much more common than any other transition or transversion. Indels and point mutations were most common, showing moderate abundance in introns, and were least common in coding regions and 3’ trailer regions of genes.