ANNInter is a collection of ncRNA-ncRNA interactions (NNIs) in Arabidopsis thaliana. NNIs are predicted using available tools, and a few are validated using high-throughput sequencing data such as degradome-seq. ANNInter also offers an efficient search option, enabling the discovery of interactions involving small to long ncRNAs with sequence data from databases including plant small RNA genes, tsRBase, RNAcentral, and PlantcircBase.