In marine settings, anthropogenic disturbances and climate change increase the rate of biological invasions. Predicting still undescribed invasive alien species (IAS) is needed for preparing timely management responses. We tested a strategy for discovering new potential IAS using DNA in a trans-equatorial expedition onboard RV Polarstern. During one-month travel, species inside ballast water experienced oxygen depletion, warming, darkness and ammonium stress. Many organisms died but several phytoplankton and zooplankton survivors resisted and were detected through a robust combination of individual sampling, DNA barcoding and metabarcoding, new in ballast water studies. Ammonium was identified as an important influential factor to explain diversity changes in phytoplankton and zooplankton. Some species reproduced until the end of the travel. These species tolerant to travel stress could be targeted as potential IAS and prioritized for designing control measures. Introducing resistance to travel stress in biosecurity risk analysis would be recommended.