A paper was done on this in 2014 by Fiorella Fernanda Mazine, Vinicius Castro Souza, Marcos Sobral, Félix Forest & Eve Lucas in KEW BULLETIN (2014) 69: 9497 DOI 10.1007/S12225-014-9497-X
A preliminary phylogenetic analysis of Eugenia (Myrtaceae: Myrteae), with a focus on Neotropical species.I've put the phylogenetic trees below. They don't include some major species like candolleana, luschnathania and selloi. Probably the most interesting finding is that uniflora and pitanga are in the same clade as brasiliensis.
Edit: I was told that E. candolleana belongs to the Racemosae section (Clade 8 on the dendrogram). I always suspected it was related to Eugenia florida.