Armored scale insects (Hemiptera: Diaspididae) are among the most invasive insects in the world. They have unusual genetic systems, including diverse types of paternal genome elimination (PGE) and parthenogenesis. Intimate relationships with their host plants and bacterial endosymbionts make them potentially important subjects for the study of co- evolution. Also, in some groups, the adult female never sheds the second instars cuticle, and remains within its confines, a habit referred to as the pupillarial habit. Here we expand upon recent phylogenetic work (Morse and Normark 2006) by analyzing a partitioned dataset including armored scale and endoysmbiont DNA from one hundred and twenty three species of armored scales, represented by two hundred and fifty-four samples. Included were fragments of the nuclear protein-coding gene Elongation Factor 1α (EF1α), the D2 and D3 expansion segments of the large subunit ribosomal RNA gene 28S, and a region of mitochondrial DNA encompassing the 3' portion of cytochrome oxidase I (COI), and the 5' portion of cytochrome oxidase II (COII). Ribosomal 16S from the primary bacterial endosymbiont Uzinura diaspidicola was amplified as well. Two versions of our dataset were analyzed due to concerns over the possible effects of missing data. The first version (the full dataset) contained all 254 taxa, with every taxon having at least both the 28S and EF1α fragments. The second version (the core dataset) had only the 113 taxa for which all four fragments were available. Maximum parsimony, maximum likelihood, and Bayesian analyses were run on both versions of the dataset, as well as individually for each fragment. We find that our results were consistent across methods, and between the two versions of the dataset. It appears that including missing data had little effect on topology. Our results mirror that of the classic taxonomy, however we reconstruct a general lack of monophyly at the subfamily, tribal, and subtribal levels. Within the two major subfamilies, we reconstruct that the same developmental pathway has evolved independently. We reconstruct independent replacements of the pupillarial habit with the scale cover, followed by independent origins of early PGE. In each case there appears to be increased diversity in clades associated with the scale cover and early PGE. In light of this apparent increase we propose a new adaptive scenario under which early PGE may have evolved – the removal of male-killing paternal chromosomes. We also reconstruct the ancestor to the armored scales to Australasian in origins, and to have an ancestral diet breath that includes members of the Rosids and/or Monocot plant groups.