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DNA barcoding identifies a species by reading a short, standardized stretch of DNA and matching it against a reference library of sequences from vouchered specimens. For animals, the standard stretch is a 650 base pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. The match is only as reliable as the library entry behind it, which is why the specimen record matters as much as the sequence.
Short answer
A DNA barcode is, in NCBI’s words, “a short nucleotide sequence from a standard genetic locus for use in species identification.” Identification works by comparison: an unknown sample’s barcode is checked against sequences that were deposited with a documented specimen. The two public resources most labs meet are the GenBank Barcode collection at NCBI and the Barcode of Life Data System (BOLD).
What a DNA barcode is
NCBI describes its Barcode collection as “a public collection of reference sequences from vouchered specimens of all species of life.” Three ideas sit in that sentence, and each one is a practical requirement rather than background:
- Short and standard. A barcode is one defined locus, not a whole genome, so that results from different labs can be compared like for like.
- Reference sequence. The barcode is only useful as a comparison point. It is not a free-standing result.
- Vouchered specimen. The sequence is tied to a physical specimen that can be re-examined. Without that tie, a sequence cannot be checked against what it was supposed to represent.
For animals, NCBI names the locus as “a 650 base pair region on the 5′ end of the mitochondrial cytochrome oxidase subunit I (COI) gene.”
How identification works in practice
BOLD Systems defines the process as “identifying species via standardized DNA genetic markers,” and states that “through this method, unknown samples are identified to species present in the reference library.” That gives the logic of the whole method:
- A standard marker region is sequenced from the sample.
- The sequence is compared with the reference library.
- The sample is assigned to a species that is represented in that library.
Both resources are public, so the reference side of this comparison is shared across labs. The quality of the answer depends on the library records, not on the instrument that produced the query sequence.
Barcode Index Numbers (BINs)
Not every sequence in a library carries a formal species name. BOLD addresses this with the Barcode Index Number: “an automated method for clustering DNA barcode sequences from animals into operational taxonomic units,” where each cluster identifier “serves as a proxy for a species.” In practice a BIN lets a lab group sequences that belong together even when no accepted species name is attached yet. As shown on BOLD’s homepage on 29 October 2026, the portal held over 21.1 million public records representing 1.7 million species.
What a barcode record must include
The most useful, and least discussed, part of barcoding for lab staff is the record around the sequence. NCBI’s Barcode Submission Tool collects “specimen voucher, geographic location, collection date, primer data, and trace files,” and prompts so “each Barcode record is complete at the time of submission.” That list works as a checklist for anyone planning to deposit or reuse barcode data:
| Record element (NCBI Barcode Submission Tool) | What it lets a later reader do |
|---|---|
| Specimen voucher | Return to the physical specimen behind the sequence |
| Geographic location | See where the specimen came from |
| Collection date | See when the specimen was collected |
| Primer data | See which primers produced the amplified region |
| Trace files | Inspect the underlying sequencing reads, not only the final sequence |
Specimen handling upstream of the sequencer therefore decides whether a barcode can be submitted at all. Labs that already track specimens as biospecimens have the voucher, place and date in hand; labs that do not should record them before the tissue is subsampled. For the consumable side of sequencing work, see the genetic testing lab supply checklist.
Barcode regions by group
NCBI states the animal standard as the COI region above. For other groups, the locus follows the reference library a lab intends to match against, so confirm the marker with that library before designing primers or ordering reagents. For how barcoding fits specific disciplines, see the CASRAI guides on zoology, entomology and mycology.
Barcoding and other identification routes
DNA barcoding identifies organisms from a sequence. Other laboratory identification routes read a different signal; for example, MALDI-TOF identifies microorganisms from a mass spectrum rather than a sequence. The two answer the same question by different evidence, and a lab choosing between them is choosing between a sequence-and-reference-library workflow and a spectrum-and-reference-database workflow. Sequence reference data of the kind barcodes feed into is also curated elsewhere at NCBI; see the CASRAI guide to the NCBI Reference Sequence database.
Common misunderstandings
A barcode is not a whole-genome result
The barcode is one short standard locus. It is used to place a sample against a library, not to describe the organism’s genome.
A sequence without a voucher is a weaker record
NCBI’s collection is built from vouchered specimens, and its submission tool asks for the voucher, location, date, primers and trace files up front. A sequence stripped of that context cannot be audited later.
An identification names only what the library contains
BOLD describes identification as assigning unknown samples to species present in the reference library. Where the library holds no matching entry, the method has nothing to assign, and a BIN may be the closest available label.
BINs are clusters, not species names
BOLD describes a BIN as a proxy for a species, produced by an automated clustering method for animal barcode sequences. It groups sequences; it does not replace a formal name.
FAQ
What is DNA barcoding used for?
Identifying a specimen to species by comparing a short standard DNA sequence with a reference library, as described by both NCBI and BOLD.
Which gene is the standard barcode for animals?
NCBI names a 650 base pair region at the 5′ end of the mitochondrial cytochrome oxidase subunit I (COI) gene.
What information goes with a barcode submission?
NCBI’s Barcode Submission Tool collects the specimen voucher, geographic location, collection date, primer data and trace files.
What is a BIN?
A Barcode Index Number, which BOLD uses to cluster animal barcode sequences into operational taxonomic units that serve as a proxy for a species.
Sources
- NCBI, GenBank Barcode (page updated 2017-11-09; checked 2026-10-29).
- BOLD Systems, Barcode of Life Data System (checked 2026-10-29).
