A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with energy metabolism, protein biosynthesis and cell-cell recognition representing either genotypic variation in gene expression or the effects of specific environmental conditions that affect patterns of energy acquisition, growth and pathogen encounters. Less variation was present between central and peripheral branches (7%) and only a single gene was deemed differentially expressed (P=1.493 x 10(-3)). The function of this gene, a phosphatidylserine decarboxylase, suggests different growth patterns between branch positions within colonies and is consistent with the usual higher growth rates on the perimeter of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels of mechanical stress and require greater levels of photo-protection associated with higher water flow and light levels. This study therefore confirms transcriptomic variation in response to small-scale environmental gradients consistent with differential resource allocation in clonal coral colonies. (C) 2009 Elsevier B.V. All rights reserved.