The Apicomplexa are a large protozoan phylum of obligate parasites that infect a wide range of invertebrate and vertebrate hosts. Within the Apicomplexa, the suborder Adeleorina is composed of some of the least understood and most biologically diverse parasites in the phylum. The occurrence of a biological process called syzygy characteristically unifies the members of the Adeleorina within the order Eucoccidiorida. The breadth and diversity represented by this group pose challenges for taxonomic classification. Investigations into the biodiversity of the Adeleorina, specifically its most biologically diverse genus Hepatozoon, were advanced in this study by generating and analyzing DNA sequences from all three genomes, nuclear, apicoplast and mitochondrial, typically found in apicomplexan protists. To accomplish this objective, new molecular tools and methods were developed. Strongly conserved regions of adeleorinid mitochondrial genomes were identified and these largely invariant regions were exploited to generate polymerase chain reaction (PCR) primers that assisted in the amplification and subsequent sequencing of a wide range of adeleorinid mitochondrial genomes. Additionally, a novel approach for ‘data mining’ parasite sequences in mixed-DNA high throughput sequence data was investigated. This method assisted in sequencing understudied targets, such as the apicoplast genome, that otherwise would have been challenging to amplify using traditional PCR techniques. The data reported in this thesis were the first complete extrachromosomal genome sequences to be reported from members of the suborder Adeleorina; in total, 48 newly generated sequences from 12 adeleorinid taxa were reported: 19 (11 complete and 8 partial) mitochondrial genome sequences, 8 (2 complete and 6 partial) apicoplast genome sequences and 21 (1 complete and 20 partial) nuclear ribosomal RNA gene unit sequences. These novel data were compared with publically available data from closely and more distantly related apicomplexan parasites. Data generated in the course of this thesis have approximately doubled the number of known apicomplexan mitochondrial genome configurations, including the longest apicomplexan mitochondrial genome to be sequenced to date. This thesis provides much needed baseline sequence data, including associated methodologies and molecular tools, to support future molecular investigations on the extrachromosomal genomes and the evolution of the biologically diverse members of the suborder Adeleorina.