HI @Jean0521, I'd be cautious about interpreting phylogenies and performing microbial community analysis from data that have been generated with different primers. 
The reason is that each primer pair will have it's own set of amplification biases, i.e. some primer pairs are better at amplifying (or not) some taxa over others. Which will skew your interpretation of which taxa are present and/or more or less abundant.
Also, you will not be ale to construct a robust phylogeny if the sequenced regions do not overlap. You'd likely have to perform closed-reference OTU picking, or use GreenGenes2 to map your reads to a sequence / phylogeny. Again, this will not remove primer biases and will lead to erroneous interpretation of your data.
I'd advise against merging the data in this way. Especially, if these samples are from different environments!
If they are from the same environments, then you can compare / contrast which primer pairs work best.