Chromosomal structure variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismalphenotype. Some of these effects are caused by structural variations containing genes. Modern sequencing using short reads makes the detection of large structural variations (> 1kb) very difficult. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of Drosophila melanogaster (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Because the average read length used for these approaches are much longer than traditional short read sequencing, these maps facilitate the identification of chromosomal SVs of greater size and with more clarity. We found a wide diversity of structural variations in each of the five strains. These structural variations varied greatly in size and location, and significantly affected exonic regions of the genome. Structural variations accounted for a much larger difference in number of base pairs between strains than single nucleotide polymorphisms (SNPs).