I would like to find taxonomic solution for the insects ie. aquatic bugs (Naucoridae) I am working with. I have already decided that I am going to approach with the genes of 16S rRNA and 28S rRNA for the aforesaid after went through the previous attempts of works related to this. Eventhough, I am looking for the valuable suggestions from the scientific communities those who are dealing with the related issues.
Ideally you should use both and then decide, as well as different outgroups and see how your trees are going. Additionally, for these kind of bugs, an integrated approach is needed (i.e. include molecular but also morphologic data). Hope this help.
The choice for genes should be based on the taxonomic range you are interested on, for instance 16S can be considered to investigate deeper nodes, e.g. between tribes or subfamilies, whereas 28S for intermediary nodes, e.g. between genera within a tribe or subfamily. If you want to investigate the relationships within a genus you should think about using COI, COII and Cyt b for better ingroup resolution, in combination with 18S and 28S for outgroup resolution.
You can find interesting results about these topics here:
https://www.jstage.jst.go.jp/article/aez/35/3/35_3_293/_pdf and http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2005.00302.x/full
I also agree with Eduardo that using an integrated approach will give you more informative results.
My opinion is - you have to chose both genes and compare the results.
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