Each ribosomal repeat (rDNA unit) consists of a pre-rRNA gene cluster (5′ETS, 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA, 3′ETS) transcribing in a single molecule and intergenic spacer (IGS) containing regulatory elements. In chicken Gallus gallus rDNA units are situated in the only Nucleolar organizer region (NOR) on chromosome 16. As in many other eukaryotes, chicken rDNA repetitive units are missing in the current version of assembled genome (GRCg6a). Our previous attempt to assemble a full rDNA unit using Illumina data was not successful due to the complex structure of repeats in IGS, only transcribed rRNA gene cluster has been deciphered (NCBI Nucleotide: KT445934). Here, we describe a chicken IGS structure basing on PacBio single-molecule sequencing of a BAC clone WAG137G04 containing chicken NOR fragment with 3 complete IGSs from one White Leghorn individual. Also, Red jungle fowl contig NT_456123.1 was included into analysis. We identified several novel tandem repeats, which form regular highly organized structures. Most of repeats are highly GC-rich (65–81%) contributing to the total IGS high GC composition (68% vs. 52% in human). IGS is heterogeneous in length due to a copy number variation of some repeats. The alignment of transcriptome reads from different chicken tissues against the most complete rDNA sequence from WAG137G4_utg0 contig has revealed a weak transcriptional activity at certain central sites of IGS We have compared the IGS organization between chicken and terrapin (Malaclemys terrapin); the complete ribosomal repeat sequence of terrapin was assembled using the raw data of sequencing. In both species, the IGS contains very long conservative GC rich tandem repeats and lack of the inverted sequence copies capable to form hairpins. It turned out that on contrast to IGS of mammals, amphibians and fish, the IGS in chicken and terrapin are GC-enriched and contain many putative CpG islands. These common features in the IGS structure appear to be significant when considering the genome evolution in the Sauropsida group. Financial and technical support : RFBR (#18–04–01276), “Chromas” and “Molecular and Cell Technologies” Resource Centres of Saint Petersburg State University, SPbU project 1.40.1625.2017.