Molecular methods have revolutionized the interrogation of natural microbial communities. Length heterogeneity PCR (LH-PCR) is an established PCR based technology that has been successfully used to study complex microbial environments in soils and sediments. Additionally, the 16s rRNA can be cloned and sequenced to determine microbial composition of the comunity, although this latter technique is time consuming and costly. Thus, we routinely use LH-PCR as a screening tool to target the more costly cloning and sequencing process. We have developed several semi-automated tools for analyzing LH-PCR fingerprint and 16S rRNA data. These consist of custom PERL scripts and a MYSQL database to automate the processing of LH-PCR data from the SCE 9610 fluorescent capillary sequencer as well as the statistical comparison of diversity indices and the calculation of refraction curves. We have also developed an automatic clone identification and abundance tabulation process based on MEGABLAST searches of the Ribosomal Database Project's 16S rRNA database. We will demonstrate these tools using LH-PCR fingerprint data from bacterial communities of the barrier island fringe marsh at the Virginia Coastal Reserve Long Term Ecological Resource where we show that the bacterial 16s rRNA fingerprints of samples from three distinct habitats (High, dry Spartina Marsh, Low wet Spartina Marsh, and adjacent mud flats) are less biologically diverse than originally hypothesized.