while I don't work in the DNA barcoding field myself, colleagues are doing it for identification from the species level up. That seems to be the most used method today. You may find more information on the web page of the "International Barcode of Life" (http://ibol.org/). There is also an active German "chapter" of ibol that I am aware of at https://www.bolgermany.de/ - you might find helpful information there, as well. And there are also the barcoding databases at http://www.barcodinglife.com/ - maybe there is already some information on the species you are interested in.
Nowadays even companies offer services in barcoding already - for example see http://www.eurofinsgenomics.eu/en/genotyping-gene-expression/applied-genomics-services/dna-barcoding.aspx (usual disclaimers: no affiliation, bla bla ...)
Hope that helps - good luck (and a Happy New Year to all!),
There is no universal method for this particular aim, but there are a lot of approaches (probably several dozens or more) to use depend on a range of factors and specific features of studied object. If you provide a bit more information about your research it can be possible to give a more exact answer.