Aphaenogaster mersa is an extinct species of ant in the subfamily Myrmicinae known from a pair of Middle Eocene fossils found in Europe.

A. mersa is one of three species in the ant genus Aphaenogaster to have been noted from fossils found in Baltic amber by William Morton Wheeler.

[1] Aphaenogaster mersa was examined and described from a single type specimen worker which was fossilized as an inclusion in a transparent chunk of Baltic amber.

[1] A third northern European amber species, A. antiqua, was described in 2009, and the authors of the 2009 paper noted a second confirmed A. mersa specimen which had been identified during their study.

The exoskeleton of A. mersa shows an overall reticulate patterning that is more rugose than A. sommerfeldti with only the frontal portion of the head capsule bearing possible longitudinal striations.