Genomic annotation is the process of locating functionally relevant regions within a stretch of DNA. Specifically, the annotation of genes includes locating gene start sites, stop sites and determining the coordinates of coding exons in addition to describing the function of these genes. The genome of Drosophila melanogaster has been entirely annotated, and is therefore an excellent reference species for the annotation of genes in related Drosophila species. The goal of the present study was to use comparative genomics to construct evidence based gene models for multiple isoforms of 8 orthologous genes present on contig10, a 50,000 base pair DNA sequence, of the 3L chromosome of Drosophila elegans. The bioinformatics tools utilized included FlyBase, Gene Record Finder, NCBI BLAST, Gene Model Checker, Small Exon Finder, and the UCSC Genome Browser Mirror. Together, these bioinformatics tools were used in conjunction with biological evidence to successfully construct high quality gene models for multiple isoforms of 8 putative orthologs present on contig10: ArfGAP3, CG32452, mael, CG14450, CG11367, CG32454, CG11241, and l(3)04053. These genes showed variable conservation relative to the putative D. melanogaster orthologs, ranging between 38.6-90.4% protein identities. Genes with known crucial ontology, such as ArfGAP3 (ADP-ribosylation factor GTPase activating protein 3) showed high conservation with D. melanogaster (%ID = 90.0%), while lesser studied genes such as CG32452 showed much lower conservation (%ID = 38.6%). The construction of high quality evidence-based gene models will contribute to the understanding of the evolution of the heterochromatic dot chromosome compared to euchromatic regions in different Drosophila species.