A social annotation model learning system (SAM-LS) was created using multiple instructional strategies thereby supporting the student in improving in critical thinking, critical writing and related literacy. There are four mechanisms in which the SAM-LS methodology is believed to improve learning and performance. These mechanisms include providing relevant activities such as (1) examples, (2) practice, (3) reflection and (4) collaboration. The Social Annotation Model uses HyLighter, an online annotation system that amalgamates reading and writing, facilitates shared annotation practices and coalesces annotations from multiple reviewers. This article reports on three studies conducted using HyLighter. The purpose of the first study was to determine student perceptions on the benefits and weaknesses of the learning environment, using HyLighter, with a focus on peer critique. The findings indicated that users' experiences were positive and specifically the annotations and tags were useful in a peer critique activity. The second study was a nonexperimental comparative study that looked at students' ability to critically analyze information and reading comprehension using HyLighter in collaborative activities. Initial findings show that working in small collaborative groups may promote deeper thinking through peer interactions. The third study was to determine whether there was a change in reading comprehension, critical thinking and meta-cognition skills from the use of SAM-LS instructional strategies. Results indicate that HyLighter may help students in several areas including enhancing the students' ability to think critically. (Contains 3 figures and 2 tables.)