Heteroplasmy is the presence of multiple genotypes in an individual and is commonly associated with mitochondria where thousands of copies of the genome can be present in a single organelle. Even in low frequencies, it can cause severe illness or death and strong selective pressures usually result in a low occurrence. Despite this, cloning and sequencing of a portion of the open reading frames of the nad2, nad4, and coI mitochondrial loci in the blue crab Callinectes sapidus (Rathbun, 1896) revealed abnormally high levels of heteroplasmy at all loci with as many as 24 haplotypes in a single individual and the dominant haplotype accounting for as little as 43.9% of the total sequences. A minimum spanning network comparing these individuals at each locus demonstrated an overlap of haplotypes between the female and themegalopa with almost no overlap of themale sequences. Illumina sequencing ofmuscle and testes froma single individual usingmultiple differentDNA-based amplificationmethods as well as cDNA amplification confirmed heteroplasmic circular mitochondrial DNA templates with portions of the reads containing unmapped highly repetitive regions at specific sequence positions in both tissue types. Thus, the blue crab appears to possess a highly degenerate and possibly fragmented mitochondrial genome that is present in germline tissue and linearly inherited. A general lack of fragmentation present in the cDNA sequences as well as site-specific sequence changes argues for mitochondrial editing as a way of maintaining sequence integrity. This is the first evidence for mitochondrial editing in a crustacean and a potential explanation for observations of extremely high population diversity when using blue crab mitochondrial markers.