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The SSU rRNA gene is one of the most widely utilized loci for phylogenetic inference among eukaryotic organisms. Although they have an average length of 1800 to 1900 bp, several unusually large 18S rDNA sequences have been reported. After examining GenBank sequences and 180 new 18S rRNA sequences from several metazoan groups, we report many other extraordinary sequences ranging between ca. 1350 bp (in symphylan myriapods) to ca. 3300 bp (in some strepsipteran insects). Myriapods are particularly interesting, having independently evolved extraordinary sequences in the four classes (Chilopoda, Diplopoda, Symphyla, and Pauropoda). An insertion event of ca. 300 bp has been detected in all but the most basal family of geophilomorphan centipedes. Other major insertions are also found in other arthropod groups, in onychophorans, molluscs, chaetognaths, echinoderms, and parasitic platyhelminths. The use of information derived from secondary structure predictions combined with a new method to analyze DNA sequence data without multiple sequence alignments is proposed as a solution for analyzing sequence data that possess alternatively conservative and variable regions, such as ribosomal genes.