This study aims to assess the distinctive characteristics of a hierarchically-designed hypermedia learning environment through students' perceptions. The study design included a total of seventeen 9th grade high school biology students in Ankara, Turkey, and lasted for 15 hours. The results of the study showed that the material promoted a feeling of empowerment. The freedom of choice and an individualized learning environment resulted in increased student motivation. The screen design, text sizes, graphics, videos and colors used in the program were very convenient. The learners were navigating in the program according to their own learning pace and choice. Their initial interest in the units did not affect their attitudes towards the hypermedia learning environment used during the experiment. Learners suggested that the hypermedia learning environment should be used together with a traditional learning environment and with the teacher.