Underreplication (replication of a portion of the total complement of DNA in each chromosome) is well documented in the highly polytene chromosomes of Drosophila ovary nurse cells, follicle cells surrounding oocytes, abdominal histoblasts, fat body cells, gut cells, and cells of the late prepupal salivary glands. Recently we found that replication in a majority of thoracic cells in D. melanogaster stall between G1 and G2, which means these cells too are underreplicated. Since variation in genome size has been shown to be linked to the amount of repeat and noncoding sequence, we ask, “Is the percentage of replication in DNA of thoracic cells directly related to the genome size of a species, and Is this consistent among species?” We also ask, “How much does the late replicating portion of the genome contribute to overall genome size evolution?” To address these questions, we estimate, using flow cytometry, the underreplication level and genome size for more than 100 Drosophilidae from the UC San Diego Species Stock Center. These data are then analyzed using traditional statistic methods as well as newer comparative phylogenetic methods in an effort to measure phylogenetic signal and rate of evolution of genome size of replicated and underreplicated DNA. The Drosophila phylogeny used for this analysis was reconstructed with the super-matrix method using Bayesian reconstruction. Preliminary results have shown that with a few striking exceptions, larger genomes of Drosophila have lower replication percentages; whereas small genomes have complete or almost complete levels of replication. These data support the conclusion that genome size change is largely, but not always, an increase or decrease in noncoding sequence. Moreover, the rate and mode of change is different for the replicated and unreplicated portions of the genome.