We report on the fabrication of Ag nanoparticle (Ag NP) decorated germanium (Ge) nanocap (Ag-NPs@Ge-nanocap) arrays protruding from highly ordered porous anodic aluminum oxide (AAO) template as highly sensitive and uniform surface-enhanced Raman scattering (SERS) substrates. The hybrid SERS substrates are fabricated via a combinatorial process of AAO template-assisted growth of Ge nanotubes with each tube having a hemispherical nanocap on the AAO pore bottom, wet chemical etching of the remaining aluminum and the AAO barrier layer to expose the Ge nanocaps, and sputtering Ag NPs on the Ge nanocap arrays. Because sufficient SERS "hot spots" are created from the electromagnetic coupling among the Ag NPs on the Ge nanocap and the highly ordered Ge nanocap arrays also have semiconducting chemical supporting enhancement, the hybrid SERS substrates have high SERS sensitivity and good signal reproducibility. Using the hybrid SERS substrates, Rhodamine 6G with a concentration down to 10(-11) M is identified, and one congener of highly toxic polychlorinated biphenyls with a concentration as low as 10(-6) M is also recognized, showing great potential for SERS-based rapid detection of organic pollutants in the environment.