Abstract
The aim of this research in to know microscopic representation change in atom and molecule concept which is influenced by STEM Education. This research is one of the sequences in Research and Development of test instrument by chemistry software. The kind of this research is fieldwork research with one group pre-test and post-test design. Subjects in this research are the twenty-seven students in MBS Senior High School grade 11 th in Yogyakarta region. STEM Education can improve student microscopic representation skill from 30.18 to 54.62 in average score and based on student result in painting molecule with ChemDraw and Avogadro's application, there are a lot of improvement in understanding concept.