Of course, I am speaking about soundly different morphospecies, thus excluding those cases in which the morphological inter-populational (inter-taxa?) differences were incorrectly "assumed" to be present.
One of the best examples is the work of Reuschel and Schubart (2006), highlighting possible mtDNA introgression between the two morphologicaly distinct species Xantho hydrophilus and X. sexdentatus.
Thank you Temim, it seems rather interesting. Also the paper by Zofkova & Timms (2009) is pertinent, and I am attaching it below for completeness' sake.
See "High connectivity and lack of mtDNA differentiation among two previously recognized spiny lobster species in the southern Atlantic and Indian Oceans" by Johan Groeneveld
Article High connectivity and lack of mtDNA differentiation among tw...
This paper looks at two species of Heptacarpus shrimps that were previously believed to be two different species. Jensen shows that they are in fact one species. Genetic techniques are not used but it may still be useful to you.
Article Heptacarpus littoralis Butler a synonym of Heptacarpus sitch...
Dear Fede, there is a paper of Jimoh et al., 2013, about two species of West African giant prawns, where molecular phylogenetic analyses revealed mtDNA clades which were not concordant with the morphology to two distinct groups recognized as morphological species. Individuals were rather clustered together due to similar environment.
Article Mismatch between molecular (mtDNA) and morphological classif...