The study presents the complete sequence and comparative analysis of sex chromosomes in five great apes (bonobo, chimpanzee, western lowland gorilla, Bornean orangutan, Sumatran orangutan) and a lesser ape (siamang gibbon). Using the telomere-to-telomere (T2T) human genome methodology, researchers generated gapless assemblies of the X and Y chromosomes for these species, revealing their evolutionary intricacies. The Y chromosomes vary greatly in size and have low alignability and high structural rearrangements due to lineage-specific ampliconic regions, palindromes, transposable elements, and satellites. The X chromosome is more stable, while the Y exhibits dynamic evolution. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of over 100 great ape individuals. These assemblies inform human evolution and conservation genetics of endangered apes. The X and Y chromosomes originated from autosomes ~170 million years ago. The X chromosome retains most of the original autosomal gene content, while the Y has acquired sex-determining genes and mutations, leading to reduced recombination and size. The human Y chromosome has ampliconic regions with extensive intrachromosomal homology and palindromes that counteract deleterious mutations. The X chromosome also has PARs, ancestral regions, and palindromes. Previous studies lacked complete ape sex chromosome assemblies, leading to fragmented and incomplete data. The T2T assemblies for six ape species revealed significant new sequences, particularly in Y chromosomes, with high frequencies of non-canonical DNA structures. Y chromosomes showed greater variation in length than X chromosomes. The Y chromosome has higher substitution rates and structural variants, indicating rapid evolution. The X chromosome has lower substitution rates and more stable gene content. Ampliconic regions and palindromes are critical for Y chromosome stability. Palindromes on the Y chromosome are longer and have higher coverage than on the X. Segmental duplications are more common on the Y chromosome. Repeats on sex chromosomes include transposable elements, satellites, and simple regions. The Y chromosome has higher repetitive element content than the X. DNA methylation patterns differ between X and Y chromosomes, with the Y chromosome showing lower methylation. Centromeres on X and Y chromosomes have evolved differently, with Y centromeres being more variable. rDNA arrays are found on Y chromosomes of some species but not on X chromosomes. Protein-coding genes on the Y chromosome show lineage-specific expansions and contractions. Some genes are under purifying selection, while others are involved in spermatogenesis. De novo genes may have emerged on the Y chromosome. Intraspecific diversity analysis showed higher diversity on the X chromosome in some species, while the Y chromosome had lower diversity. The study highlights the dynamic evolution of the Y chromosome, with palindromes and ampliconic regions playing key roles in maintainingThe study presents the complete sequence and comparative analysis of sex chromosomes in five great apes (bonobo, chimpanzee, western lowland gorilla, Bornean orangutan, Sumatran orangutan) and a lesser ape (siamang gibbon). Using the telomere-to-telomere (T2T) human genome methodology, researchers generated gapless assemblies of the X and Y chromosomes for these species, revealing their evolutionary intricacies. The Y chromosomes vary greatly in size and have low alignability and high structural rearrangements due to lineage-specific ampliconic regions, palindromes, transposable elements, and satellites. The X chromosome is more stable, while the Y exhibits dynamic evolution. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of over 100 great ape individuals. These assemblies inform human evolution and conservation genetics of endangered apes. The X and Y chromosomes originated from autosomes ~170 million years ago. The X chromosome retains most of the original autosomal gene content, while the Y has acquired sex-determining genes and mutations, leading to reduced recombination and size. The human Y chromosome has ampliconic regions with extensive intrachromosomal homology and palindromes that counteract deleterious mutations. The X chromosome also has PARs, ancestral regions, and palindromes. Previous studies lacked complete ape sex chromosome assemblies, leading to fragmented and incomplete data. The T2T assemblies for six ape species revealed significant new sequences, particularly in Y chromosomes, with high frequencies of non-canonical DNA structures. Y chromosomes showed greater variation in length than X chromosomes. The Y chromosome has higher substitution rates and structural variants, indicating rapid evolution. The X chromosome has lower substitution rates and more stable gene content. Ampliconic regions and palindromes are critical for Y chromosome stability. Palindromes on the Y chromosome are longer and have higher coverage than on the X. Segmental duplications are more common on the Y chromosome. Repeats on sex chromosomes include transposable elements, satellites, and simple regions. The Y chromosome has higher repetitive element content than the X. DNA methylation patterns differ between X and Y chromosomes, with the Y chromosome showing lower methylation. Centromeres on X and Y chromosomes have evolved differently, with Y centromeres being more variable. rDNA arrays are found on Y chromosomes of some species but not on X chromosomes. Protein-coding genes on the Y chromosome show lineage-specific expansions and contractions. Some genes are under purifying selection, while others are involved in spermatogenesis. De novo genes may have emerged on the Y chromosome. Intraspecific diversity analysis showed higher diversity on the X chromosome in some species, while the Y chromosome had lower diversity. The study highlights the dynamic evolution of the Y chromosome, with palindromes and ampliconic regions playing key roles in maintaining