This study aims to investigate the comparison of motivation and learning achievements of students who were taught by using E-learning based schoology and power point media on human reproduction system in grade XI IPA SMA Negeri 1 Silimakuta. The research method which was applied was quasi experiment with the participans of all students of grade XI IPA are 160 students. The sample of research was determined by cluster random sampling technique mainly grade XI-1 was taught by using E-learning based schoology media and grade XI-2 was taught by using power point media. The research design which was used was pretest-posttest control group design. Data analysis technique used Independent Samples t Test. The result of the research showed that there was comparison of students' learning motivation which was taught by using Elearning based schoology media (89.67 ± 3.06) and by using power point media (85.63 ± 3.45) was 4.72% (tcount4.95; P = 0.000). There was comparison of the students' learning achievements which was taught by using E-learning based schoology media (85.44 ± 5.58) and by using the power point media (72.53 ± 7.93) was 17.79% (tcount7.249; P = 0.000). These results indicated that the use of E-learning based schoology media more contributes to improve students' motivation and learning achievements, especially in the material of the human reproduction system. Thus, researchers suggested that the use of E-learning based schoology media in the process of biology learning as one of the learning innovation efforts.