Vaucheria is a genus of yellow-green algae, the taxonomy of which is based on the morphology of antheridia and oogonia. Distribution of Vaucheria in New Zealand is poorly understood. Only two studies have investigated phylogenetic relationships in the genus world-wide and these omitted some of the diversity found in New Zealand. We identified seven species of Vaucheria based on morphology of their reproductive structures. Two were described as new species (V. aestuarii and V. edaphica), two were reported for the first time from New Zealand (V. erythrospora and V. litorea), one has been reported previously (V. bursata), and the identification of the remaining two was inconclusive (Vaucheria cf. borealis and Vaucheria cf. conifera). The genetic variation and phylogenetic position of these species were studied using phylogenetic analyses of rbcL sequences. These showed the existence of morphologically indistinguishable cryptic species complexes in sect. Corniculatae. Our results were mostly consistent with the current morphology-based sectional classification of the genus.