Generally I need to confirm that all the oligochaetes I have belong to one species. What do think about molecular markers I have to use? As I know specialists often use 18s-RNA gene or COI gene for Oligochaetes phylogeny. What about ITS for instance?
I would suggest any of the following COI, 12S, 16S, ITS and H3. COI is probably the most well used one, but it is prone to divide the sequences into to many clusters, 12S and 16S both seems to work fine they are easy to amplify. ITS is usually a bit trickier, the primers available do not work for all taxa, but if you can get good quality sequences it should work fine. H3 is the most conservative of all the regions I have suggested but seems to be able to distinguish between closely related taxa.
I think for your question COI is OK. 18S is almost invariable on species level (at least in earthworms). 16S works well but more conservative that COI. ITS is really hard to amplify. So I would use COI first and if somehow it doesn't work try 16S.
About BAR-coding gaps in Annelida there is a great paper by Kvist, S. : Does a global DNA barcoding gap exist in Annelida? Mitochondrial DNA. 2014 Nov 28:1-12.
Good Luck!
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