This research aimed to improve critical thinking ability and reduce misconception on ecology material in the students of X MIPA 1 of SMA Negeri 5 Surakarta in the school year of 2014/2015 through the application of e-module based on Problem-Based Learning. This study was a Classroom Action Research conducted in two cycles, each of which consisting of four stages: planning, acting, observing, and reflecting. The subject of research was the students in X MIPA 1 of SMA Negeri 5 Surakarta in the school year of 2014/2015 consisting of 30 students. Techniques of collecting data used were essay test to measured critical thinking skill, open ended reasoning of two-tier diagnostic test to measure misconception, observation and interview as the data proponents. Data validation was conducted using triangulation methode. The data were analyzed using descriptive qualitative technique consists of three components: data reduction, data presentation, and taking the conclusion. Target of the research is an increase of 20% on critical thinking aspects and reduce misconception 20% on ecology concepts at the end of the cycle. The result of research showed that there were an increase in critical thinking ability and a decrease in misconception. The improvement of critical thinking ability included six aspects: interpretation of 20.83%, analysis of 20.42%, evaluation of 40.00%, conclusion of 39.17%, explanation 32.50%, and self regulation of 25.83%. The decreased misconception included four important concepts in ecology: population of 34.45%, community of 43.06%, food chain and web of 34.07%, and science, environment, technology and community (salingtemas) ecology of 28.15%. Considering the result of research, it could be concluded that the application of e-module based on Problem-Based Learning could improve critical thinking ability and reduce the students' misconception in ecology material.