We present CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows closely-spaced binding sites to be called accurately. We apply CSDeconv to novel ChIP-seq data for DosR binding in Mycobacterium tuberculosis and to existing data for GABP in humans and show that it can discriminate binding sites separated by as few as 40 bp.