The internal transcribed spacer 2 (ITS2) is a phylogenetic marker, which can be used over a broad range of phylogenetic distances. Even though the ITS2 evolves rapidly on the sequence level, its secondary structure is highly conserved throughout the eukaryotes. The power of the ITS2 marker comes from combined sequence-structure alignments allowing phylogenetic tree reconstructions in a noticeable extent of taxonomic levels. Here we present the ITS2 database, which provides sequence and structure information of ITS2 and several analytical tools. Currently the database contains 112.000 ITS2 sequences and secondary structures, of which 100.000 were determined using a homology modelling approach. Accompanying tools are provided allowing the user to analyse their own ITS2 sequences and structures. An HMM-based annotation tool provides delineation and verification of start and end positions of ITS2 sequences within the rRNA precursor. ITS2 structure prediction is carried out by homology modelling on the entirety of sequences present in the database or by user supplied template structures. From here 4SALE automatically builds a combined sequence-structure alignment, which can be loaded into ProfDistS in order to reconstruct phylogenetic trees. Further analytical possibilities include the search for compensatory base changes (CBCs) in pairwise sequence-structure alignments via the CBCAnalyzer. CBCs are currently discussed as a possible marker for detection of species boundaries.