AthaMap provides a genome-wide map of potential transcription factor and small RNA binding sites (TFBS) in Arabidopsis thaliana. Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites. Matrix- and pattern-based screenings were performed to identify potential transcription factor binding sites in the genome of Arabidopsis thaliana (TAIR release 8). The complete list of the 211 transcription factors included in AthaMap and the corresponding references and screening results are displayed on the Documentation page. By using the Search function, the sequence of a specific genomic position or gene can be displayed in a sequence window including the potential transcription factor binding sites. A Colocalization function allows the search for user-defined potential combinatorial elements. A set of pre-calculated known combinatorial elements is already incorporated in AthaMap. The Gene Analysis tool enables identification of common transcription factor binding sites and small RNA target sites in a set of user-submitted genes. The Gene Identification tool allows the search for genes harbouring specific transcription factor binding sites. All genes targeted by smallRNAs and miRNAs are identified in AthaMap when the web-tools Colocalization, Gene-Analysis, and Gene Identification are used. Putatively small RNA targeted genes are shown in italics, putatively miRNA regulated genes are shown in bold. The MicroRNA Targets function permits the identifcation of target genes for miRNAs. 190 screening sequences corresponding to the 243 miRNA genes and the number of genomic hits can be found on the the Documentation page. The Small RNA Targets function enables identification of small RNA targets from different small RNA libraries given on the Documentation page.