Author summary We observe an excess of detrimental mutations, consistent with genomic meltdown in woolly mammoths on Wrangel Island just prior to extinction. We observe an excess of deletions, an increase in the proportion of deletions affecting gene sequences, and an excess of premature stop codons in response to evolution under low effective population sizes. Large numbers of olfactory receptors appear to have loss of function mutations in the island mammoth. These results offer genetic support within a single species for nearly-neutral theories of genome evolution. We also observe two independent loss of function mutations at the FOXQ1 locus, likely conferring a satin coat in this unusual woolly mammoth.