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Reflection and transmission modes are studied in a surface plasmon resonance (SPR) sensor, where a nanohole-array-patterned gold film is deposited on a glass substrate, and the analyte in an aqueous medium is bound onto the patterned gold film. The reflection (transmission) mode means that light illuminates the structure from the analyte (substrate) side, and the detection is fixed at the analyte side. The two modes are studied by calculating absorption (and transmission) spectra and optical field distributions of the sensor. This study shows that both modes can excite the SPR on the analyte/gold interface, which is useful for sensing. However, the optical field distribution at the resonant wavelength is different for the two modes, and the effect is dependent on the gold film thickness. Comparing the sensing performance, the reflection mode gives larger resonant optical field enhancements (32 as compared with 22), but the transmission mode uses much thinner gold films (60 nm as compared with 150 nm). The optical power flow is analyzed to understand the fundamental difference between the two modes. These findings are particularly useful to guide the design of metallic nanostructure-based plasmonic sensing systems.