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Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multiprimer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high\u2010volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging\n                    <jats:italic>Bemisia<\/jats:italic>\n                    pest cryptic species complex as examples. The whiteflies\n                    <jats:italic>Bemisia<\/jats:italic>\n                    including the\u201d\n                    <jats:italic>tabaci<\/jats:italic>\n                    \u201d species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multiprimer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test\u2010species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field\u2010testing our redesigned\n                    <jats:italic>Bemisia<\/jats:italic>\n                    metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub\u2010Saharan Africa 1\n                    <jats:italic>Bemisia<\/jats:italic>\n                    putative species as the dominant pest species, with other cryptic\n                    <jats:italic>Bemisia<\/jats:italic>\n                    species being detected at various abundances. We also provide evidence that\n                    <jats:italic>Bemisia<\/jats:italic>\n                    species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multiprimer HTS metabarcoding method incorporated two overlapping amplicons of 472\u00a0bp and 518\u00a0bp that spanned the entire 657\u00a0bp 3' barcoding region for\n                    <jats:italic>Bemisia<\/jats:italic>\n                    , and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving transboundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high\u2010density, cryptic, pest\u2010species complexes.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13576","type":"journal-article","created":{"date-parts":[[2021,12,17]],"date-time":"2021-12-17T03:23:26Z","timestamp":1639711406000},"page":"1706-1724","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A high\u2010throughput amplicon sequencing approach for population\u2010wide species diversity and composition survey"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8451-0811","authenticated-orcid":false,"given":"Wee Tek","family":"Tay","sequence":"first","affiliation":[{"name":"CSIRO Black Mountain Laboratories  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