The R-loop, a three-stranded nucleic acid structure composed of an RNA:DNA hybrid and a displaced single-stranded DNA, plays versatile roles in many physiological and pathological processes. However, its controversial genomic localization and incomplete understanding of its regulatory network raise great challenges for R-loop research. Here, we present R-loopBase to tackle these pressing issues by systematic integration of a huge amount of genomics and literature data. A reference set of human R-loop zones is computed with confidence scores and detailed annotations (Search, Help and Download), all of which can be visualized in well-annotated genomic context in a local genome browser (Browser). A list of 1,185 R-loop regulators is manually curated from PubMed literatures and annotated with most up-to-date multi-omics data (Regulator). We have also manually curated 24 R-loop regulators in mouse, 63 in yeast (saccharomyces cerevisiae) and 21 in Escherichia coli to facilicate R-loop research in these model organisms (Regulator). We further deduce the functional relationship between individual R-loops and their putative regulators (Regulator and Download). In total, we have generated billions of entries of functional annotations, which can be easily accessed in our user-friendly interfaces (Help). The regulator summary and genomic annotation of R-loop regions will be constantly updated along the research progress of field. You are welcome to contribute to updating R-loop regulators and related literatures (Regulator Updating System on Regulator page). Any suggestions and feedbacks from you are also welcome (Contact).