Under some population genetic models, asexual lineages are expected to accumulate deleterious mutations. Evidence of mutation accumulation has recently been reported from Daphnia, in which the mitochondrial genomes of obligately parthenogenetic lineages have an increased rate of amino acid replacement. Here we investigate whether similar effects are seen in armored scale insects, by comparing protein coding sequences of paired sexual and parthenogenetic lineages, using mitochondrial, nuclear and endosymbiont loci. Our aim is to understand why parthenogenetic lineages have a higher extinction rate than sexual lineages, which is an important question in evolutionary biology. Because many insect pests are parthenogenetic, understanding their vulnerability to extinction may ultimately prove to have importance for pest management as well.