I am working on the taxonomy of Nematodes, so for molecular characterization I want to choose molecular markers from mitochondrial genes or nuclear genes or have to work on both the genes.
For nuclear gene u can try with ITS and first 2 domain of LSU (D1D2), and for Mitochondrial gens u can try with CO1 gene. But amplifying fast evolving gene is sometimes very difficult with universal primer,,, so we need to design new primers if the universal primer is not working.
I would say the answer depends on your group. I don't know about Nematodes, but I believe in Vertebrates for example the mitochondrial genes evolves faster in average than the nuclear ones. By contrast, octocorals have very low variation in mitochondria, so much than the COI gene often is not useful at all in shallow taxonomic levels.
Still I would argue that the mitochondrial genes normally evolve faster in animals simply because of smaller effective population sizes.
The 18S rRNA (SSU) has been broadly sequenced for many nematode taxa and has a resolution down to the species level in most groups, but also resolves higher relationships quite well. General primers usually work and it is quite easy to get good sequences for the SSU. Apart from the SSU the mitochondrial COI would likely be your second choice, see the second papers I have attached. The paper nicely shows that a combination of the SSU with a second (e.g. LSU, COI) marker sufficently resolves species level complexes in root knot nematodes.
Article A phylogenetic tree of nematode based on about 1200 full-len...
Article Comparison of two short DNA barcoding loci (COI and COII) an...
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