The study aims to recognize the level of metacognition skills in the e-learning environment and Learning Motivation among students of Sultan Qaboos University and the relationship between them, with the research on the differences in the levels based on the gender variable (male – female), and the type of faculty (scientific colleges - literary colleges). The sample of the study consisted of (497) students from the undergraduates' level for academic year 2020/2021: (169) males and (328) females. To meet study objectives, the researcher used two tools: scale of metacognition skills in e-learning environment (Eladl, 2003) and scale of learning motivation (Eladl, 2017), and its validity, reliability and suitability to the Omani environment were confirmed through the sample survey. The results of this study showed low and medium levels of metacognition skills in e-learning environment, and medium level of learning motivation among students. The results also revealed a positive statistically significant correlation between metacognition skills in e learning environment and learning motivation. Also, the study indicated that there were statistically significant differences in metacognition skills in e-learning environment based on the gender for the benefit of males in monitoring skill and statistically significant differences for the benefit of scientific colleges in monitoring skill.