Second Generation Biofuel Producer Tax Credit Act of 2009 - Amends Internal Revenue Code provisions relating to the cellulosic biofuel producer tax credit to: (1) revise the applicable amount of such credit by linking it to the British thermal unit (BTU) content of second generation biofuels as determined by the Secretary of the Treasury; (2) expand the definition of "qualified feedstock" to include any cultivated algae, cyanobacteria, or lemna; (3) exclude from the definition of "second generation biofuel" certain fuel produced from coprocessing with nonqualified feedstocks and certain unprocessed fuels; (4) require producers of second generation biofuels to register with the Secretary; and (5) allow an additional depreciation allowance for property used to produce second generation biofuel.