Historically, chromosome number has been one of the first pieces of information collected about an organism's genome. These numbers have been shown to vary widely across organisms (Blackmon and Demuth 2015, Perkins et al. 2019, Sylvester et al. 2020, Morelli et al. 2022). Chromosome numbers change due to fission events, where chromosome number increases, and fusion events, where chromosome number decreases. As Drosophila species have been used as model organisms for nearly a century, there is an abundance of information on chromosome number, chromosome shapes, and sex chromosome systems. Chromosome shapes are described as rod (telocentric), j (submetacentric), v (metacentric), and dot (small and heterochromatic). Sex chromosome systems present in this genus include the XY, X0, and neo-sex chromosome systems. There are more than 1,600 species of Drosophila identified and classified into two large subgenera which have diverged for 40-65 million years: Drosophila and Sophophora. Recently, Drosophila genus karyotype data were compiled into an open source database (Morelli et al 2022). While there is a plethora of information on chromosomes in the Drosophila genus, no work has specifically focused on the rates of chromosome number change in this genus. To address this problem, I am using comparative phylogenetic analyses through the chromePlus package in R (Blackmon et al., 2019) with a previously published phylogeny of 152 species in the Drosophila genus (Hjelmen et al., 2019). Specifically, I am investigating how the rate of chromosome number and shape evolution differs between subgenera and sex chromosomes systems. Through these methods, I am able to compare the rates of fusion and fission between the groups of interest. In the future, these methods will be expanded to the entire Diptera order. These works contribute to the growing body of knowledge on chromosome and genome structure evolution.