16S rRNA and Amplicon Sequencing Market (2026-2036)

The growth of this market is mainly driven by the widespread use of 16S rRNA and ITS amplicon sequencing in microbiome research, the adoption of targeted amplicon-based NGS panels for oncology and inherited disease testing, the use of amplicon sequencing for viral genome surveillance and drug resistance testing, and the low cost and simple workflows of amplicon methods compared with whole-genome approaches. In addition, the introduction of full-length 16S and ITS sequencing on long-read platforms, the approval of amplicon-based companion diagnostics with rapid turnaround, the use of amplicon sequencing for genotyping in agriculture and food testing, and the verification of gene editing in cell and gene therapy development are further supporting the growth of this market.

The 16S rRNA and Amplicon Sequencing Market, also referred to as the targeted amplicon sequencing market, amplicon-based NGS market, or marker gene sequencing market, comprises the kits and reagents, instruments, software, and services used to amplify and sequence specific regions of DNA or RNA. Amplicon sequencing uses PCR to enrich target regions before sequencing, providing a low-cost, sensitive, and simple approach for analyzing selected genes. The market includes 16S rRNA gene and internal transcribed spacer (ITS) sequencing for profiling bacterial and fungal communities; targeted human gene panels for oncology hotspot mutations, inherited disease, and pharmacogenomics; pathogen amplicon sequencing for viral genome surveillance and drug resistance; amplicon-based genotyping for plant and animal breeding and food testing; and the use of amplicon sequencing to verify gene editing. It includes amplicon panels, primers, library preparation kits, and reagents; short-read and long-read sequencers; analysis software; and sequencing services. The market ecosystem extends from reagent and panel developers and sequencing platform providers to service laboratories, clinical laboratories, academic and public health researchers, pharmaceutical and biotechnology companies, and agricultural and food companies.

The market is experiencing steady growth because amplicon sequencing offers an efficient balance of cost, sensitivity, and simplicity. By focusing sequencing on regions of interest, amplicon methods require less sequencing capacity than whole-genome or shotgun approaches, work with small amounts of input DNA, and can detect low-frequency variants. These advantages make amplicon sequencing well suited to large microbiome studies, routine clinical testing of tumor samples with limited tissue, rapid viral genome sequencing, and high-throughput genotyping.

Microbiome research is one of the largest applications of amplicon sequencing. 16S rRNA gene sequencing remains the most widely used method for profiling bacterial communities in human, animal, and environmental samples because of its low cost and established analysis methods, while ITS sequencing is used to profile fungi. Long-read sequencing is enabling full-length 16S and ITS sequencing, which improves taxonomic resolution to the species level. In September 2025, Oxford Nanopore Technologies launched the Microbial Amplicon Barcoding Kit 24 V14 for full-length 16S rRNA gene and full-length ITS sequencing of bacteria, archaea, and fungi, with support for custom primers and a sequencing-ready library in about one hour after PCR, enabling same-day microbial profiling results. PacBio offers Kinnex 16S kits for high-throughput full-length 16S sequencing, and Zymo Research provides full-length 16S library preparation kits and microbial community standards. At ASM Microbe 2026, Zymo Research highlighted microbial community standards, metagenomic reference materials, and benchmarked extraction and library preparation workflows, emphasizing the need to reduce lysis bias and improve the reproducibility of microbiome sequencing.

Targeted amplicon panels are widely used in clinical oncology. Amplicon-based NGS panels detect hotspot mutations, small insertions and deletions, and fusions in genes such as EGFR, KRAS, BRAF, and PIK3CA, guiding the selection of targeted therapies. In July 2025, Thermo Fisher Scientific received U.S. Food and Drug Administration (FDA) approval for the Oncomine Dx Express Test, a targeted amplicon-based NGS test that detects mutations across 46 genes on the Ion Torrent Genexus Dx Integrated Sequencer with results in as little as 24 hours, as a companion diagnostic for ZEGFROVY (sunvozertinib) in non-small cell lung cancer with EGFR exon 20 insertion mutations and for tumor profiling in solid tumors. Pillar Biosciences received FDA premarket approval for its oncoReveal Dx Lung and Colon Cancer Assay, an amplicon-based NGS test, and amplicon panels from Illumina, QIAGEN, and Integrated DNA Technologies are widely used in clinical and research laboratories. The ability of amplicon methods to work with small biopsy samples and deliver rapid results is particularly valuable for treatment decisions.

Amplicon sequencing is also central to pathogen genomics. Tiled amplicon approaches were the primary method used to sequence SARS-CoV-2 genomes during the COVID-19 pandemic and are now used for influenza, RSV, mpox, and other viruses, while targeted amplicon sequencing is used to detect drug resistance mutations in HIV and Mycobacterium tuberculosis. In agriculture and food testing, amplicon-based genotyping supports plant and animal breeding, and amplicon metabarcoding is used for food authenticity and environmental DNA monitoring.

At the same time, the market faces competition from shotgun metagenomic sequencing, hybrid capture panels, and whole-genome sequencing, which are becoming more affordable and provide broader information. Amplicon methods can also be affected by PCR bias, primer mismatches, and limited ability to detect copy number changes and novel fusions. As a result, providers that improve accuracy, resolution, and workflow speed, and that integrate amplicon sequencing with long-read and automated platforms, are expected to capture the largest share of growth over the forecast period.