The Checklist of non-native freshwater fishes in Flanders, Belgium is a species checklist dataset published by the Research Institute for Nature and Forest (INBO). It contains information on 23 alien fish species occurring in Flemish natural and semi-natural waterbodies, detected in sampling between 1992 and 2006. This species checklist was assessed within the framework of the Freshwater Fish Monitoring Network by Verreycken et al. (2007) and reassessed for Verreycken et al. (2018). Here it is published as a standardized Darwin Core Archive and includes for each species: the scientific name, kingdom, and stable taxon identifier (in the taxon core), the Dutch and English vernacular name (in the vernacular names extension), the year of first introduction and last assessment in Flanders (given as a year range in the event date in the distribution extension), coarse habitat information (in the species profile extension) and the pathway(s) of introduction, native range(s), and invasion stage in Flanders (in the description extension). The dataset can be used for researching and managing aquatic invasions or compiling regional and national registries of alien species. Issues with the dataset can be reported at: https://github.com/trias-project/alien-fishes-checklist We have released this dataset to the public domain under a Creative Commons Zero waiver. We would appreciate it if you follow the the INBO norms for data use (https://www.inbo.be/en/norms-data-use) when using the data. If you have any questions regarding this dataset, don’t hesitate to contact us via the contact information provided in the metadata or via https://twitter.com/LifeWatchINBO. This dataset was published as open data for the TrIAS project (Tracking Invasive Alien Species http://trias-project.be, Vanderhoeven et al. 2017), with technical support provided by the Research Institute for Nature and Forest (INBO). It is selected as one of the authoritative sources for the compilation of a unified and reproducible checklist of alien species in Belgium.