Biological systems respond not only to chemical stimuli (drugs, proteins) but also to physical stimuli (light, heat, stress). Though there are many high throughput tools for screening chemical stimuli, no such tool exists for screening of physical stimuli. This paper presents a novel instrument for photonic high throughput screening of photosynthesis, a light-driven bioprocess. The optical microplate has a footprint identical to a standard 96 well plate, and it provides temporal and intensity control of light in each individual well. Intensity control provides 128 dimming levels (7-bit resolution), with maximum intensity 120 mE/cm(2). Temporal modulation, used for studying dynamics and regulation of photosynthesis, can be as low as 10 μs. We used photonic screening for high throughput studies of algal growth rates and photosynthetic efficiency, using the model organism Dunaliella tertiolecta, a lipid producing algae of interest in biofuel production. Due to the ability to conduct 96 studies in parallel, experiments that would require 2 years using conventional tools can be completed in 1 week. This instrument opens up novel high throughput protocols for photobiology and the growing field of phenomics.