Key points at a glance

• If you compare only the letters (A, C, G, T) at positions that line up cleanly between the species, humans and chimpanzees match for roughly 98.5% to 99% of those letters.
• If you also count DNA that doesn’t line up well — including insertions, deletions and duplicated segments — overall similarity drops to roughly 96%–97%.
• Some parts of the genome are much more different (for example, the Y chromosome), while many protein-coding sequences are nearly identical.
• Big biological differences often come not from letter-for-letter changes alone but from changes in gene regulation, copy number, and genome structure.

Where did the “~99%” figure come from?

The modern version of this claim traces to the first high-quality comparisons of human and chimpanzee genomes. When researchers aligned long stretches of human DNA with their chimp counterparts, they found that only about 1.2% of the aligned letters differed — implying ~98.8% identity within those aligned regions. That result echoed even earlier protein-level studies showing that many human and chimp proteins are nearly the same.

It’s a compelling factoid: two species that look and behave so differently differ by only about one letter in a hundred across much of the genome. But the fine print matters. That ~1.2% figure ignores pieces that refuse to line up cleanly, and it counts only single-letter changes, not insertions, deletions, or bigger rearrangements.

What does “sharing DNA” actually mean?

There isn’t a single, universal yardstick for “percent similarity.” Genomes differ in many ways, and each way you choose to count will give you a slightly different number. Here are the main approaches researchers use and what each captures.

1) Single-nucleotide identity in alignable regions

This is the cleanest apples-to-apples comparison: line up the parts of the human and chimp genomes that can be aligned with high confidence, then ask what fraction of those positions carry the same base. By this metric, humans and chimps are roughly 98.5%–99% identical — the origin of the famous number.

Pros: precise and reproducible in high-confidence regions. Cons: ignores DNA that doesn’t align well (which is often where structural differences live).

2) Including insertions and deletions (indels) and unalignable DNA

Once you include “gaps” — stretches present in one species but not the other — the fraction of DNA that is shared shrinks. Indels and unalignable segments collectively account for additional differences beyond the ~1.2% single-letter changes. With these counted, genome-wide similarity commonly lands around 96%–97%.

Pros: a more complete picture of what’s actually shared. Cons: estimates vary with the quality of genome assemblies and how aggressively you treat repeats and duplications.

3) Gene content and copy number

Another way to compare genomes is to ask: do both species have the same genes, and in similar copy numbers? Here, humans and chimps are broadly similar — the vast majority of genes are shared — but not identical. Each lineage carries lineage-specific gene duplications and losses. For instance, humans have gained or expanded copies of some genes implicated in brain development and synapse formation.

Pros: focuses on parts of the genome most obviously tied to function. Cons: misses crucial differences in when and where genes turn on (regulation).

4) Chromosome-scale structure

Genome architecture also differs. The most famous example is human chromosome 2, which formed by the fusion of two ancestral ape chromosomes. Other differences include inversions, segmental duplications, and especially pronounced divergence on the Y chromosome, which shows extensive rearrangement and gene-content turnover between the species.

Pros: captures big, functionally meaningful changes. Cons: hard to boil down to a single “percent similar” number.

Why newer genome assemblies matter (and what they don’t change)

Genome comparisons keep improving as reference assemblies get more complete. The human “telomere-to-telomere” reference now includes previously missing repetitive regions, and primate genomes continue to be upgraded as well. These advances tune estimates of similarity — particularly in repeat-rich, structurally complex regions — but they don’t overturn the core picture: near-99% identity in aligned letters, lower overall similarity once you count insertions, deletions, and duplicated DNA.

If DNA is so similar, why are humans and chimps so different?

Small genomic changes can have outsized effects when they land in the right places. Several mechanisms help explain how modest differences yield large biological contrasts:

• Regulatory DNA changes: Many differences lie in enhancers and other regulatory elements that control where, when, and how strongly genes are expressed. Distinct gene expression programs, especially in the developing brain, can produce big phenotypic effects.
• Gene duplications and losses: Extra copies of genes (or partial duplications that create new variants) can rewire pathways. Human-specific duplications have been implicated in cortical development and synaptic function.
• Structural variation: Insertions, deletions, and rearrangements can alter 3D genome architecture and bring genes under new regulatory control.
• Post-genomic layers: Epigenetic marks, RNA editing, alternative splicing, and protein-level modifications add complexity beyond the DNA letters.

In short, a one-number summary of DNA similarity doesn’t capture the many ways genomes encode and regulate biology.

So, is “~99% shared DNA” correct?

It’s a useful, memorable shorthand — with caveats. If you mean “of the positions that align cleanly, what fraction are the same letter,” then yes, it’s close to 99%. If you mean “what fraction of the entire genome is identical when you include insertions, deletions, and duplicated segments,” then the number is a few points lower, roughly in the mid-90s. Both statements can be accurate, depending on the yardstick.

Two things are unequivocal: humans and chimpanzees are each other’s closest living relatives, and their genomes are strikingly similar by any vertebrate standard. At the same time, the differences, though modest in percentage terms, are more than enough to account for the distinct biology of each species.

Further reading

• Initial sequence of the chimpanzee genome and comparison with the human genome (Nature, 2005)
• Great ape genetic diversity and population history (Nature, 2013)
• Chimpanzee and human Y chromosomes are remarkably divergent (Nature, 2010)
• Complete human genome sequence (Science, 2022)
• Human accelerated regions and regulatory evolution (Nature, 2006)
• King and Wilson revisited: molecular similarities and regulatory differences (PNAS background)