We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives. ### Competing Interest Statement E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. C.T.W. is a co-founder/CSO of Clareo Biosciences, Inc. W.L. is a co-founder/CIO of Clareo Biosciences, Inc. The other authors declare no competing interests. * AQER : ancestor quickly evolved region cDNA : complementary deoxyribonucleic acid CDR : centromere dip region CRE : cis-regulatory element DJ : distal junction [region] ENC : evolutionary neocentromere ERV : endogenous retrovirus FLNC : full-length non-chimeric GGO : gorilla HAQER : human ancestor quickly evolved region [human branch] HAS : human HiFi : high-fidelity HOR : higher-order repeat ILS : incomplete lineage sorting LINE : long interspersed nuclear element LTR : long terminal repeats MEI : mobile element insertion MHC : major histocompatibility complex mya : million years ago ncRNA : noncoding RNA Ne : effective population sizes NHP : nonhuman primate NOR : nucleolar organizer region NUMT : nuclear sequence of mitochondrial DNA origin ONT : Oxford Nanopore Technologies ORF : open reading frame PAB : Sumatran orangutan PacBio : Pacific Biosciences Inc. PGGB : pangenome graph builder PLE : Penelope-Like Retroelements PPA : bonobo PPY : Bornean orangutan PTR : chimpanzee PWS : Prader-Willi syndrome RC : rolling circle repeats rDNA/rRNA : ribosomal deoxyribonucleic/ribonucleic acid SD : segmental duplication SDR : structurally divergent region SF : suprachromosomal family SINE : short interspersed nuclear element SNV : single-nucleotide variant SVA : SINE-VNTR-Alu element T2T : telomere-to-telomere TE : transposable element TOGA : Tool to infer Orthologs from Genome Alignments UL : ultra-long VNTR : variable number tandem repeat