The study aimed to measure the validity of critical thinking instruments and determined the differences in critical thinking skills in terms of gender and knowledge group. The study was used survey method. Critical thinking instruments were developed based on the Facoine's (2015) indicators of critical thinking. Data were obtained from 285 respondents (N = 285) of first-year students who took Indonesian language courses. Respondents consisted of 78 male and 207 female students. The 25 questions in critical thinking instruments were claimed valid and homogeneous with r count of 0.266. Data were analyzed using nonparametric statistics of Mann-Whitney test in SPSS version 21 application for Windows. There was no significant difference in students' critical thinking skills in gender differences and knowledge groups. Result of the study showed that 22 sub-indicators of students' critical thinking was found similarity in gender and 20 sub-indicators also found similarity in knowledge group. The study supported the new paradigm that students regardless of gender differences and science clusters needed critical thinking skills. Based on learning context in various science groups, there was no need to differentiate gender even though there were differences in the number of a certain gender in one class.