Paederinae, a diverse subfamily of rove beetles (Staphylinidae), is poorly explored with an outdated subtribal and generic classification lacking proper phylogenetic perspective. Therefore, the discovery of two Baltic amber fossil specimens resembling the genera Micrillus and Scymbalium, which are particularly challenging in terms of systematics, called for a thorough analysis to infer their phylogenetic position and their ecological requirements. The fossils were examined with light microscopy supplemented by X-ray micro-computed tomography, and then scored into a Paederinae-specific matrix of 99 morphological characters, along with a broad sample of recent Paederinae and non-paederine outgroups. Morphological phylogenetic analyses were conducted, using Bayesian Inference and Maximum Parsimony. The obtained phylogeny confirmed that the genera Scymbalium and Micrillus form a lineage outside Lathrobiina; therefore, both genera are now classified as Lathrobiini incertae sedis pending a more inclusive phylogenetic work on Paederinae. The analysis firmly placed both fossils in that recent lineage, albeit rendering Micrillus paraphyletic with respect to Scymbalium. Without a more extensive analysis based on the revised world fauna, any systematic changes would be premature. Thus, the fossils are described as Micrillus electrus, sp. nov. and Scymbalium phaethoni, sp. nov. in accordance with the current diagnoses of both genera. Given that the recent species of Micrillus and Scymbalium are predominantly thermophilic and mainly confined to dry open landscapes in Africa, southern Eurasia and Australia, the finding of Baltic amber representatives implies the very diverse landscape and the equable (sub)tropical palaeoclimatic conditions of the Eocene amberiferous ‘forest’, the latter being the subject of continued debates.