Summary Cyst nematodes of the genus Heterodera are obligatory sedentary endoparasites of great economic importance throughout the world. The Goettingiana group of this genus consisted of 17 species parasitising dicotyledons and are characterised by a lemon-shaped cyst having an ambifenestrate cone, long vulval slit, weak underbridge and presence or absence of bullae. In this study, we provided comprehensive phylogenetic analyses of 164 COI and 108 ITS rRNA gene sequences of several species of the Goettingiana group, including H. carotae, H. circeae, H. cruciferae, H. goettingiana, H. microulae, H. persica and H. urticae and several unidentified species using Bayesian inference, maximum likelihood, and maximum and statistical parsimony. 126 new COI and 46 new ITS rRNA gene sequences from 45 nematode populations representing six valid and two unidentified species collected in 13 countries were obtained in this study. Heterodera scutellariae syn. n. is considered as a synonym of H. circeae based on similar molecular and morphological characters. The carrot cyst nematode H. carotae is reported in France on a wild carrot species growing in natural ecosystems and in California from an agricultural field for the first time. The nettle cyst nematode in Spain and France is also reported for the first time. Our study showed that the ITS rRNA gene sequence can be used for discrimination of some species from the Goettingiana group; however, it did not allow differentiating H. carotae, H. cruciferae and H. urticae belonging to the H. cruciferae species complex from each other. The COI gene sequences clearly distinguished all studied species of the Goettingiana group from each other and can be recommended as a DNA barcoding marker for this group. It has been hypothesised that the majority of the Goettingiana group species originated and diversified in regions located in Western and Eastern Asia and Central and Western Europe during the Pleistocene and then dispersed from these regions across the world.