The purpose of this study was dual: First, to develop and validate assessment schemes for assessing 11th grade students' meaningful understanding of organic chemistry concepts, as well as their systems thinking skills in the domain. Second, to explore the relationship between the two constructs of interest based on students' performance on the applied assessment framework. For this purpose, (a) various types of objective assessment questions were developed and evaluated for assessing meaningful understanding, (b) a specific type of systemic assessment questions (SAQs) was developed and evaluated for assessing systems thinking skills, and (c) the association between students' responses on the applied assessment schemes was explored. The results indicated that properly designed objective questions can effectively capture aspects of students' meaningful understanding. It was also found that the SAQs can elicit systems thinking skills in the context of a formalistic systems thinking theoretical approach. Moreover, a significant relationship was observed between students' responses on the two assessment strategies. This research provides evidence that students' systems thinking level within a science domain is significantly related to their meaningful understanding of relative science concepts.