The bioluminescence tomography is a novel molecular imaging technology for small animal studies. Known reconstruction methods require the completely measured data on the external surface, although only partially measured data is available in practice. In this work, we formulate a mathematical model for BLT from partial data and generalize our previous results on the solution uniqueness to the partial data case. Then we extend two of our reconstruction methods for BLT to this case. The first method is a variant of the well-known EM algorithm. The second one is based on the Landweber scheme. Both methods allow the incorporation of knowledge-based constraints. Two practical constraints, the source non-negativity and support constraints, are introduced to regularize the BLT problem and produce stability. The initial choice of both methods and its influence on the regularization and stability are also discussed. The proposed algorithms are evaluated and validated with intensive numerical simulation and a physical phantom experiment. Quantitative results including the location and source power accuracy are reported. Various algorithmic issues are investigated, especially how to avoid the inverse crime in numerical simulations. (c) 2007 Optical Society of America.