HIV's genetic instability means that sequence similarity can illuminate the underlying transmission network. Previous application of such methods to samples from the United Kingdom has suggested that as many as 86% of UK infections arose outside of the country, a conclusion contrary to usual patterns of disease spread. We investigated transmission networks in the Resina cohort, a 2,747 member sample from Nordrhein-Westfalen, Germany, sequenced at therapy start. Transmission networks were determined by thresholding the pairwise genetic distance in the pol gene at 96.8% identity. At first blush the results concurred with the UK studies. Closer examination revealed four large and growing transmission networks that encompassed all major transmission groups. One of these formed a supercluster containing 71% of the sex with men (MSM) subjects when the network was thresholded at levels roughly equivalent to those used in the UK studies, though methodological differences suggest that this threshold may be too generous in the current data. Examination of the endo- versus exogenesis hypothesis by testing whether infections that were exogenous to Cologne or to Dusseldorf were endogenous to the greater region supported endogenous spread in MSM subjects and exogenous spread in the endemic transmission group. In intravenous drug using group subjects, it depended on viral strain, with subtype B sequences appearing to have origin exogenous to the Resina data, while non-B sequences (primarily subtype A) were almost completely endogenous to their local community. These results suggest that, at least in Germany, the question of endogenous versus exogenous linkages depends on subject group.