ABSTRACT: Conserved noncoding sequences (CNS) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with 4 dicotyledonous plant species (Arabidopsis thaliana, Carica papaya, Populus trichocarpa and Vitis vinifera), we have detected hundreds of CNS upstream of Arabidopsis genes. Distinct positioning, length and enrichment for transcription factor binding sites suggest these CNS play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of CNS-associated genes is consistent with the hypothesis that together they form part of a core transcriptional network, whose function is to regulate other transcription factors and control development in A. thaliana. We have identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.