In this study heteroplasmy genotyping of green sea turtles, Chelonia mydas, using high throughput sequencing (HTS) was used to better understand SNP and mtSTR in the mitochondrial genome and its variation within individuals across generations. HTS allows for the observing of mtDNA on the repeating the D-loop, which is not under strong selective pressure. Heteroplasmy is the existence of mitochondrial DNA (mtDNA) variant within a cell. Mitochondrial DNA is 0.001% of genomic content and due to oxidative phosphorylation, mutations that occur in mtDNA are directly associated to inherited diseases. Since heteroplasmy deals with variation in mtDNA the haplotypes passed down to generations, the mtDNA comes from maternal inheritance. Population sizes green turtles will determine the variation in haplotypes especially depending on the amount of female turtle populations. The maternal inheritance of mtDNA has a large influence on heteroplasmy due to the number of mitochondria passed, the DNA inherited and mutations along with it. Due to mtDNA being only maternally inherited and the low population sizes of green turtles, the passed down mtDNA has low genetic diversity, low mutation rates, and low rates of new generations. A shift in haplotypes from maternal inheritance will signal genetic bottlenecking during oogenesis meaning heteroplasmy will increase with larger populations and decrease in diversity with smaller populations. This study found haplotypes in individuals of green turtles in foraging grounds more than nesting sights meaning there mixing of stocks and the HTS revealed that heteroplasmy is low in frequency among these individuals.