MOTIVATION:The cis-defensins are a superfamily of small, cationic, cysteine-rich proteins, sharing a common scaffold, but highly divergent sequences and varied functions from host-defence to signalling. Superfamily members are most abundant in plants (with some genomes containing hundreds of members), but are also found across fungi and invertebrates. However, of the thousands of cis-defensin sequences in databases, only have a handful have solved structures or assigned activities. Non-phylogenetic sequence-analysis methods are therefore necessary to use the relationships within the superfamily to classify members, and to predict and engineer functions. RESULTS:We show that the generation of a quantitative map of sequence space allows these highly divergent sequences to be usefully analyzed. This information-rich technique can identify natural groupings of sequences with similar biophysical properties, detect interpretable covarying properties, and provide information on typical or intermediate sequences for each cluster. The cis-defensin superfamily contains clearly-defined groups, identifiable based on their biophysical properties and motifs. The organization of sequences within this space also provides a foundation of understanding the ancient evolution of the superfamily. AVAILABILITY AND IMPLEMENTATION:A webtool for exploring and querying the space is hosted at TS404.shinyapps.io/DefSpace. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.