Despite their cosmopolitan occurrence and massive plankton sampling during expeditions, the genetic diversity within Pteropoda Cuvier, 1804 is still largely unexplored. In this study we present a next-generation environmental barcoding approach to zooplankton bulk samples, which were collected during the circumglobal 2010 Malaspina expedition to evaluate pteropod diversity. We introduce a technique that avoids destructive procedures and leaves material intact for further morphological investigations. We extracted DNA out of the dregs (organic material such as mucus or body parts) of 27 sample containers for molecular barcoding (average 100-260 bp of COI). We were able to identify 7128 operational taxonomic units corresponding to the species composition contained in the examined samples. Among them were three species of thecosome pteropods, Creseis acicula, Creseis virgula and Cavolinia inflexa, which are discussed with respect to their taxonomy and their geographic distribution. Unidentified gymnosomes were also present in our samples from warmer regions in oceanic waters of the southern Indian Ocean. To facilitate identification of species, it is beneficial to create a better database of pteropod COI barcodes. Furthermore, gathering environmental barcoding data on a broad global scale will help to better understand species abundance and distribution of pteropods in the world’s oceans, and potentially those of other planktonic organisms.