Lampreys and hagfishes, the only living jawless vertebrates, are thought to be among the most primitive groups of vertebrates. The phylogenetic position of lampreys promises to reveal information about the origin of the vertebrate genome as well as the origin of the vertebrate body plan. Conversely, sea lamprey (Petromyzon marinus) has been a destructive invasive species in the Great Lakes since the early 20th century. Several techniques have been employed to control invasive sea lamprey; however, they are expensive and have some limitations. As a result, genetic control options that provide a theoretically powerful and effective pest control option are being investigated. Only a few studies have examined the genetic basis of sex determination, gonad differentiation, and sexual maturation in lampreys. Therefore, the objective of this study was to identify genes associated with both sex- and stage-specific gonadogenesis in the sea lamprey, including both differential gene expression (DGE) and exon usage (DEU), as well as to conduct genome-wide comparisons. RNA sequencing was performed on 28 gonad samples of male and female sea lamprey. A genome-wide DGE analysis was performed to compare differences in gene expression between sexes and between gonadal stages within sex, while DEU analyses were performed to identify sex- and stage-specific exon usage. About 14% (2617) of the total 18,945 genes were identified to be novel genes which were not annotated before. Comparison of DGE between sexes identified 4590 genes that were upregulated in females and 6088 genes that were upregulated in males. Late-stage males and females exhibited more DGE and had higher mean gene expression than early and mid-stage males and females. Moreover, chromosome 81 and 177 unassembled scaffolds were found to be part of the germline-specific region jettisoned from the somatic genome during programmed genome rearrangement, and 638 germline-specific genes were identified which showed male-biased expression pattern overall. Both the genes and exons present in the somatic and germline genomes might have potential roles in male and female development. Therefore, this thesis can be used to identify candidate genes involved in sea lamprey sex determination and differentiation which could ultimately serve as potential targets for sea lamprey control.