A taxonomic treatment is presented for all Polygala L. species of northern Australia (north of 26°S). In total, 45 species are treated, of which 44 are native and 36 are endemic to Australia. Twenty-six new species and four new varieties are described. A key to all 50 Australian species is provided, including six introduced species (five of which are restricted to southern states of Australia and are not treated here in detail). Lectotypes are here designated for five names. Nomenclatural issues regarding P. linariifolia Willd., P. glaucoides L. and P. triflora L. are discussed.