Microorganism attachment to any newly submerged surface lays the foundation for all forthcoming waves of colonization. The initial recruitment of bacteria and archaea may help guide successive settlement events through subtle assemblage variances. The detection of these changes in microbial consortia from early to mature stages in marine biofilm growth can be achieved through the use of various DNA fingerprinting tools, namely TRFLP (termination restriction fragment length polymorphism) for archaea and ARISA (automated ribosomal intergenic spacer analysis) for bacteria. These techniques allow relatively rapid snapshot assessment of diversity with reasonable resolution, at least to the genus level. Rock and synthetic slides were suspended on an array just above the sediment surface, with an identical array mirrored ten meters above in the water column. For a comparative approach, water and sediment cores were also collected. DNA from slides at various time points, from a few days to several months out, was extracted and fingerprinted to determine microbial diversity. Our results show differences in assemblages from all four environmental compartments, with operational taxonomic units (OTU) unique and common to each. Temporal differences were also observed. Shared OTUs, across the four environments showed significant variation in peak intensities, whereas replicates within compartments showed a relatively high degree of similarity. These results in conjunction with our present cloning effort will enable identification of the dominant and many of the less dominant species at various stages of marine biofilm development.