Important knowledge gaps remain with regards to the ecology and the systematics of New Zealand’s native earthworms. With many putative new species yet to be described, often specimens cannot be named, which makes species inventory, monitoring and community comparisons difficult. Our work aimed to identify new putative taxa of New Zealand native species of earthworms, and describe their distribution in selected human-modified ecosystems. A total of 24 earthworm taxa (13 native and 11 exotic) were identified using a DNA barcoding approach focusing on 16S rDNA and COI (cytochrome oxidase subunit 1). The combination of morphological and molecular analyses were complementary in elucidating species identity. However, of the 13 native taxa, eight could not be named and are likely to be undescribed species from the genera Octochaetus, Maoridrilus and Deinodrilus. Most native species appeared to have a restricted geographic distribution linked to soil conditions, in particular pH and organic matter.