CyanoCis is a database of cyanobacterial cis-acting regulatory elements. Cis-acting regulatory elements (conserved DNA motifs) were predicted computationally by comparative phylogenetic foot-printing. Conserved DNA motifs were represented as consensus sequences in the database. These motifs were predicted by comparative analysis of the upstream regions of conserved genes and clusters of orthologous transcriptional units (COT) of 14 selected cyanobacterial species. Several cis-acting elements predicted by this method were previously described experimentally. In addition to previously described ones many new conserved motifs were identified in this study, would be targets for experimental validation. We will be updating the database with new experimentally identified cis-regulatory elements from various labs. New cis-acting elements can be sent to firstname.lastname@example.org for incorporating them into the database. The new ones will be added to the database after curation. Using CyanoCis one can identify orthologs for a given cyanobacterial gene, retrieve upstream DNA sequence of any gene from all 14 cyanobacterial species and retrieve the putative cis-acting element. In addition, co-regulated genes having similar kind of conserved DNA motif can be retrieve from CyanoCis database. In the construction of CyanoCis, we have used the methods such as 'Bi-directional Best Hits' for identification of orthologs, MEME suite and several programs written in PERL and Shell scripting in our laboratory for identification of cis- acting elements and co-regulated genes.