identical fasta taxonomy


I’m classifying my amplicons using wang method with default parameters but I have a doubt : in my Reference fasta taxonomy 2 or 3 sequences are different in nucleotides composition respect to total length (they are different species), but they are identical in the region (length) of my amplicon so I wonder which will be the taxonomical assignation in this case?
Of course it is impossible a correct assignation but it isn’t clear, for me, which specie name will be assigned .

thanks in advance

It is likely that you won’t get as good of resolution with shorter reads as longer reads for this reason - not all regions are equally informative when it comes to assigning the taxonomy.