The purpose of this paper was to study and map the intellectual structure of Iranian physicists using author co-citation technique during 1990-2009. The results of the study showed that Iranian physicists have produced 6290 documents indexed in Science Citation Index (SciSearch) during the studied period. Publication counts have grown at an approximate rate of 24/70 % per year. Setare M.R. with 121 documents was the most productive Iranian author in this study. Applied Physics, with1564 documents was the most interesting subject area for the Iranian physicists. We identified 42 Iranian and international physicists who were highly co-cited in 6290 documents during the studied period. Using principal components analysis, 8 subject factors were extracted. The subject areas of factors were in: "Physics, Particles & Fields", "Astronomy & Astrophysics", “Physics, Mathematical", “Physics, Multidisciplinary", "Physics, Nuclear", "Cosmology", "Physics, Atomic, Molecular & Chemical", and "Physics, Fluids & Plasmas". The PFNet map of the intellectual structure of Iranian physicists in SciSearch during 1990-2009 showed a central subject area in "Physics, Particles & Field" with Witten E. as its focal author. The other clusters were rooted in this essential cluster.