Reciprocal teaching (RT) has been used to improve English as Foreign Language (EFL) students' reading comprehension in face-to-face instruction. However, little was known about how they use the RT to comprehend English texts in an online environment. This study explored how the implementation of RT strategies with the use of an annotation tool to improve low-achieving students' English reading comprehension in an online environment. A total of 22 low-achieving EFL students participated in this study. The pre- and post-reading comprehension tests showed that the students' English reading comprehension improved after practicing RT strategies with annotation tools. Questioning and predicating strategies were ranked as the two most useful strategies, as both promoted successful collaborative reading among students. Summarizing and clarifying were less useful than questioning and predicting strategies because the low-achieving EFL students faced language difficulties when summarizing and clarifying. The annotations supported RT strategies by (1) establishing a collaborative environment for students to discuss RT strategies any time, (2) organizing and indexing reading content in multimodal forms, and (3) helping students review and revise their comprehension.