Family Fabaceae has about 730 genera and 19.400 species. Some plant of family Fabaceae are known to have activity as an anti-breast cancer. This study does a series of computational chemistry method in virtual or in silico screening to compounds in the plant of family Fabaceae that are Abrus schimperi, Caesalpinia bonduc, Dalbergia vacciniifolia, Eriosema robustum, Erythrina falcata, Flemingia macrophylla, Genista saharae, Trifolium pratense L., Pachyrhizus erosus and Pissum sativum. The aim of this study is to find candidates of compounds as active ligands on estrogen receptor alpha (ER-α) by in silico and elucidating the amino acids contained in the binding site of compounds by using virtual screening. This protocol uses operating system LINUX Ubuntu LTS 14.04 with integrated applications such as SPORES, PLANTS 1.2, BKChem, Open Babel, R Computational Statistics and PyMOL, ZINC 01914469 as comparator compound, 4-[4-hydroxy-3-(prop-2-en-1-yl) phenyl]-2-(prop-2-en-1-yl) as reference compound and 4-hydroxytamoksifen as positive control. The results of virtual screening conducted on 60 compounds from ten plant of family Fabaceae obtained 24 compounds are actively in the binding pocket of ER-α. The important amino acids to affinity compounds with estrogen receptor alpha (ER-α) is GLU353, ARG394, ASP351 and THR347.