Evolutionary theory constitutes the overarching concept in biology. There is hardly any other concept that is more complex, and causes more difficulties in learning and teaching. One instructional approach in optimizing the learning of complex topics is to use worked examples combined with self-explanation prompts that fit to the prior knowledge (knowledge adapted prompts). Especially from cognitive psychological research we know, that prior knowledge is a tremendously relevant factor for learning. However, corresponding studies so far mainly consider the domain specific prior knowledge of high knowledge (expert) versus low knowledge (novice) students. The majority of the learners in a classroom--namely students between these experts and novices--were hardly focused on. These students will be considered here. The aim of our study was to identify how these learners with average prior knowledge can be supported by prompts when learning with worked examples. Using worked examples we analyzed how different types of self-explanation prompts (at novice and/or expert level) affect knowledge acquisition in evolution of learners with average prior knowledge. For determining the prior biological knowledge we used a general biological content knowledge test (GBCK). The learning gain was measured with an evolutionary biological content knowledge test (EBCK). Knowing what type of prompt is most effective for the learners with average knowledge we compared the benefits of this instructional combination between the three knowledge levels: novices, averages, and experts. Results show that for learners with average knowledge, all types of prompts were equally effective. The Matthew effect was not reliable between the knowledge levels. According to our results, learners with average prior knowledge did not require explicit measures of differentiation for learning evolution with prompted worked examples. Nonetheless, for the experts it seems not appropriate to use worked examples with adapted self-explanation prompts. Rather it may be advisable to use another instructional format than worked examples.