8 Minutes
the 99% claim and what it really means
It's commonly repeated in textbooks and popular media that humans and chimpanzees share about 98.8% to 99% of their DNA. That short statement captures a real genetic closeness: humans, chimpanzees and bonobos descend from a recent common ancestor relative to other primates. But the simple percentage masks a complex reality of genome structure, alignment methods and biological function. It's important for science communicators and readers to understand what the number refers to, how it is calculated, and why more complete comparisons can produce substantially larger estimates of difference.
How scientists compare genomes
DNA sequences are made from four nucleotides — adenine (A), cytosine (C), guanine (G) and thymine (T). A mammalian genome can be thought of as a string of these letters about 3 billion characters long. When researchers say two genomes are, for example, 98.8% identical, they typically mean that for alignable regions of the genome the single-letter (nucleotide) identity is about 98.8%. In other words, if you line up matching stretches of sequence, roughly 1 out of 100 nucleotides differs on average between the two species in those regions.
David Haussler, scientific director at the UC Santa Cruz Genomics Institute, has summarized this analogy as comparing two versions of a very long novel, with one being slightly edited relative to the other. Early genomic comparisons used this approach, focusing on regions that could be reliably aligned, and yielded the widely quoted ~98.8% figure.
Why that percentage is misleading
The headline percentage excludes many kinds of genomic differences that are difficult to represent as single-letter substitutions. Structural differences — insertions, deletions, duplications, inversions and mobile element activity — move chunks of DNA around or change copy number. Segments that are present in one species but absent in the other cannot be aligned in a meaningful one-to-one way, so they were often ignored or downweighted in early comparisons.
Tomas Marques-Bonet, head of the Comparative Genomics group at the Institute of Evolutionary Biology in Barcelona, notes that sections of human DNA without a clear chimpanzee counterpart make up roughly 15–20% of the genome. When alignments include those harder-to-compare regions, overall genomic difference estimates climb to roughly 5–10%, and accounting for still more complex regions may push the true overall difference beyond 10%.
A comprehensive 2025 comparison that attempted a direct, complete genome-to-genome assessment reported approximately 15% difference between human and chimpanzee genomes. That study also highlighted extensive variation within chimpanzees themselves, with differences among individual chimps reaching as much as 9% when measured the same way.
Where most differences occur: noncoding DNA and regulatory changes
The majority of genomic differences between humans and chimpanzees are concentrated in noncoding DNA — the roughly 98% of the genome that does not encode proteins. Noncoding regions include regulatory sequences, enhancers, promoters and other control elements that determine when, where and how genes are expressed.
Katie Pollard, director of the Gladstone Institute of Data Science and Biotechnology, emphasizes that regulatory regions can act like switches, modulating gene activity. A single nucleotide change or a structural change within these control regions may substantially alter gene expression patterns during development, in the brain, or in other tissues. Because proteins themselves are largely conserved, differences in gene regulation help explain large phenotypic differences between species despite high sequence similarity in protein-coding genes.
Biological significance: small changes, large effects
Why do small changes in DNA sometimes lead to big differences in anatomy, behavior or physiology? Much of the answer lies in gene regulation and developmental timing. A mutation in a regulatory element can change the spatial or temporal pattern of a gene's expression — for example, turning a gene on earlier or later in embryonic development, or activating it in a different tissue. Developmental programs are sensitive to timing and dosage, so regulatory changes can cascade into substantial phenotypic differences.
As David Haussler notes, alterations in expression driven by relatively small DNA changes can amplify through development to produce large differences in traits such as body size, hair distribution or brain organization. In short, humans and chimpanzees largely use the same molecular tool kit (proteins), but the tools are applied differently.
Methods, technologies and future prospects
Technical advances are changing our ability to compare genomes. Long-read sequencing, optical mapping, pangenome assemblies and improved algorithms for structural variant detection allow scientists to resolve previously intractable regions. These methods reveal insertions, deletions, duplications and repetitive elements that short-read alignment approaches overlooked.
Better assemblies also make it possible to measure intra-species diversity more accurately. The 2025 study that reported up to 9% variation among chimpanzees underlines that species-level averages mask extensive population-level variation — a factor important for conservation genetics, anthropology and evolutionary biology.
Looking forward, comprehensive pangenomes for humans and other primates will provide richer maps of variation, showing which segments are shared, which are variable, and which are lineage-specific. Those resources will improve our understanding of human evolution, disease susceptibility and developmental biology.
Implications for science communication and education
The shorthand '99% identical' has educational value as a memorable statement about evolutionary relatedness. However, educators and journalists should be careful to clarify what that figure represents and why more nuanced metrics matter. Focusing only on single-letter substitutions simplifies a complex genomic landscape and can obscure the roles of structural variation and regulatory divergence.
Accurate public messaging should describe both the closeness and the meaningful differences between species. Doing so helps people appreciate evolutionary relationships while understanding why small genomic changes can have outsize functional consequences.
Expert Insight
Dr. Elena Rivera, an evolutionary geneticist at a major research university, provides a practical perspective: 'Percent identity is a useful entry point, but modern genomics is about context. We now ask not just how many letters match, but where differences occur, whether they affect regulation, and how variation is distributed within and between populations. That context is critical for connecting genotype to phenotype.'
Dr. Rivera adds that emerging technologies are democratizing access to high-quality genome assemblies, which will rapidly refine our estimates of how similar or different genomes are across primates.
Related technologies and areas of research
Key tools shaping this field include long-read sequencing platforms (which capture large structural variants), high-quality reference and pangenome assemblies, CRISPR-based functional assays to test regulatory elements, and single-cell transcriptomics to map expression changes across tissues. Together these approaches allow researchers to move from descriptive comparisons to functional tests of how specific differences affect development and physiology.
Conclusion
The claim that humans and chimpanzees share nearly 99% of their DNA captures a real evolutionary closeness but omits important complexities. When comparisons are limited to alignable regions, single-nucleotide identity approaches 98–99%. When structural differences, insertions and deletions, and hard-to-align regions are included, overall genomic divergence estimates rise — studies suggest values from about 5–15% depending on methods and how variation within species is handled. Most differences concentrate in noncoding regulatory regions, and small sequence changes in these areas can produce large phenotypic effects by altering gene expression. As sequencing and assembly technologies continue to improve, our quantitative picture of human-chimpanzee genomic similarity will become more precise, deepening our understanding of evolution, development and what makes each species unique.
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