AbstractSequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed completeITS1andITS2sequences in 62 species from 16 Deuterostomia classes, withITSssequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for bothITSlength and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in bothITSswithin the same species, thymine content decrease in sense DNA sequences of bothITSsare shown. A possible role of GC-based gene conversion in DeuterostomiaITSsevolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion intoITSsequence in Deuterostomia is described in turtleGeochelone nigra.The roles of mobile genetic element insertions in the evolution ofITSsequences in some Sauropsida taxa are discussed as well.