This study was conducted in order to analyze the relation between analytical thinking skill and scientific argumentation in physics learning. The study was conducted with the interactive CK 12 simulation about optics. The sample of the study consists of 28 randomly selected students in Yogyakarta, Indonesia. The data was collected using pre and post-test after learning in the class. Data was analyzed with descriptive statistic instruments along with t-test, MANOVA test and Correlation Analysis. Research findings show that analytical thinking skill and scientific argumentation of the students are rather low. Problem based learning with web based simulation can enhance student's scientific argumentation and analytical thinking skill. Also, the correlation analysis conducted to determine the relationship between analyses analytical thinking skill and scientific argumentation. The results indicate that there is a statistical significant relationship between the analytical thinking skill and scientific argumentation.