Sex chromosomes are found throughout many diverse lineages across the animal and plant kingdom. Most of the sex chromosomes that have been studied are well established and have already experienced many evolutionary forces, making it difficult to reconstruct the dynamic changes involved in the evolution of sex chromosomes. Sex chromosomes are evolved from a pair of autosomes with closely linked sex determining genes that have stopped recombining. Papaya has many qualities that make it attractive for studying sex chromosome genetics. It is trioecious (male, female, and hermaphrodite) with sex determined by a pair of nascent sex chromosomes approximately 7 million years old. The genome is relatively small (442.5 Mb) and the sex determining region of the sex chromosomes is small and well characterized; the hermaphrodite and male specific region of the Yh and Y chromosome respectively is 8.1 Mb and the corresponding X is 3.5 Mb. These sex specific regions of the X and Y chromosomes not only contain the genes that control sex type, but they also have genes associated with the different sexes. While the vegetative forms of the three sexes are phenotypically identical, the reproductive structures are unique. In stark contrast to female and hermaphrodite flowers on male plants are borne on long pendulous peduncles (60-90 cm) at the leaf axis. Female and hermaphrodite flowers are borne on short peduncles (0-4 cm). Gynodioecious varieties SunUp, SunUp Diminutive mutant and dioecious AU9 were used to test the response of papaya to gibberellic acid (GA3). Gibberellic acid is a hormone known to cause elongation of stems throughout the plant kingdom. It is also known as a masculinizing hormone. Exogenous applications of GA3 on female and hermaphrodite papaya did not yield any sex reversals but there was a significant increase in peduncle length and inflorescence branch number in all treated plants. There was an increase in plant height for all treated plants except SunUp Diminutive mutant, suggesting that the mechanism causing the dwarf phenotype is independent of gibberellins. Gibberellin metabolism genes were identified in the papaya genome, none of which mapped to the sex-determining region of either the male- or hermaphrodite-specific region of papaya Y or Yh chromosome. We hypothesize that a trans-acting regulatory element that enhances gibberellin biosynthesis plays a role in the extreme length of the male papaya peduncle Sex chromosomes experience several evolutionary forces. To further study the structure of the sex chromosomes, a mapping population was created to generate a high density genetic map. A female AU9 was crossed with a hermaphrodite SunUp, the resulting offspring was backcrossed to the hermaphrodite SunUp. Fifty-one individuals derived from this cross were used to create restriction-site associated DNA sequencing (RAD-seq) libraries. A total of 228 RAD-seq markers were mapped to 9 major and 2 minor linkage groups. Previous studies have shown that the Y chromosome experiences severe recombination suppression along the sex determining region. The resulting map from this study showed that the X chromosome is not experiencing recombination suppression. Additionally, possible centromere locations were identified for the other chromosomes. Sex chromosomes also undergo degeneration of genetic material. The effective population size of the sex chromosomes is reduced compared to the autosome. The lack of recombination, especially for the Y chromosome also increases the rate of degeneration. RNA seq data was generated using flower and leaf tissue from females, males, and hermaphrodite individuals to determine the rate at which the Y chromosome is experiencing degeneration. Expression levels were compared between the X and Y linked alleles in males and hermaphrodites. If there is no Y degeneration, then the expression levels between the sex linked alleles should be equal. Expression of male leaf tissue had significantly less expression of the Y allele compared to the X allele. This was not found in hermaphrodites and in all flower tissue. Dosage compensation is a phenomenon utilized by many organisms with sex chromosomes to account for the heterogametic sex having only one allele for many of the genes on the sex chromosome. While many organisms compensate expression levels in the heterogametic sex, this is not true of all animals. Very few studies have been conducted to determine if plants undergo the same evolutionary forces as animals and also evolve dosage compensation. There was no detectable dosage compensation in the primitive papaya sex chromosome.