This study aimed to analyse the influence of web-based learning and learning independence toward student's scientific literacy on chemistry learning of molecule shapes. This study was conducted in a private secondary school in Jakarta, Indonesia in the odd semester of the 2018/2019 academic year. The research method used was a quasi-experiment design treatment by level 2x2. The research participants were 32 students from a 10th grade Science class consisting of 16 students from an experimental group and the other 16 students from a control class chosen by a simple random sampling technique. In the experimental class applied web media learning was used, while in the control class used applied traditional media. The test instruments used in this study were a learning independence questionnaire and a science literacy test. The results of the study showed that web media positively influenced science literacy compared to traditional media. A connection between the use of web media and learning independence towards science literacy was identified. The use of web media had a positive influence on students' scientific literacy when used in groups of students who had high learning independence but provided lower literacy results in students who had low learning independence.