Approximately ten to 15 generations after first inoculation, two invasive goby species Neogobius melanostomus and Ponticola kessleri have dispersed and established rapidly the upper Danube River. Population genomic amplified length polymorphism (AFLP) data show that the genome of the more recent newcomer, i.e. the globally invasive N. melanostomus, is significantly differentiated to a comparatively large degree (~ 5%) and exhibits pronounced small-scale population structure along a recently invaded 200 km river section. MtDNA haplotype identity over N. melanostomus samples suggests that an admixture of phylogenetically strongly differentiated source populations is unlikely. Fine-scaled local genetic population structure of N. melanostomus as deduced from Bayesian assignment tests suggest a trisection of the upper Danube instead of a clinal pattern: one downstream sample is assigned together with distant upstream samples to one population cluster. A second cluster comprises central samples, whereas two samples from the margins of this central region appear to have mixed ancestry. AFLP genome scan results indicate this population structure is strongly correlated with extrinsic (geographic) parameters, i.e. migration barriers of anthropogenic origin. However, divergence of at least one AFLP locus correlates positively with a proxy for trophic differentiation, i.e. variation of white muscle δ15N stable isotope signature. In contrast to N. melanostomus, no significant population differentiation was detectable in P. kessleri along the analyzed invasion pathway. In genome scans of P. kessleri, variation of a single locus is strongly positively correlated with an extrinsic parameter combination but not with any ecological parameter.