Abstract Inverted repeats (IRs) serve as potential biomarkers for genomic instability, DNA replication and other genetic processes. However, little information can be found in databases to help researchers recognize potential IR nucleotides, explore junction sites and annotate related functional genes. Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21 433 IRs, 113 plants chloroplast genomes, 16 948 functional genes and 21 659 visual maps. This database offers an online prediction tool for detecting IRs based on DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features.