We analyze the secondary structure of two expansion segments (D2, D3) of the 28S rRNA gene from 527 chalcidoid wasp sequences (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This comparative approach yielded 36 helices that are comprised of base pairs exhibiting positional covariation. Several regions are also involved in hydrogen-bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction (REC) or regions of slipped-strand compensation (RSC). Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment (RAA) based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.