This java-based software blasts each sequence that you provide it, and then looks for a consensus taxon among the top-hits returned from blast.
Briefly, MARTA uses NCBI's megablast program to align your sequence(s) against a local installation of blast. Then MARTA uses GenInfo Identifiers from the top-hits to retrieve taxonomic information from NCBI's taxonomy database. Using your thresholds/cutoffs, MARTA 'votes' to find a taxonomic assignment by consensus; MARTA might resolve some sequences to species level, and others to kingdom or to no level, depending on the taxonomic information held within your tag or sequence.
URL: http://bergelson.uchicago.edu/software/marta
Publication: MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences in Bioinformatics, 2010
Sounds like very similar to MEGAN, I would prefer megan for ease of use and maturity.
I should probably add MEGAN as well. I started up an unofficial rule that any time I read a question on a tool that I have not heard of I will add it to the tool section.