This study sought to determine the levels of conceptual understanding of undergraduate students regarding organic compounds within different functional groups. A total of 60 students who were enrolled in the Department of Secondary Science and Mathematics Education of a Faculty of Education at a state university in Turkey and who had followed an Organic Chemistry Laboratory Course participated in the study. The data were collected using two tools: functional group worksheets and concept maps. Both qualitative and quantitative evaluations were used in analyzing the data. The findings showed that the students generally had low levels of understanding of concepts relating to functional groups, and they exhibited a considerable number of misconceptions. Considering the findings more fully, it was determined that students have remarkable misconceptions and low levels of understanding about certain topics regarding functional groups, including the physical properties of functional groups, intermolecular bonds, acidity and basicity, reduction and oxidation, stereoisomerism and structural isomerism, and aromaticity and aliphaticity, as well as other organic chemistry concepts (e.g. decarboxylation, oxyacide, and phenol). The results suggest that since students are unable to adequately comprehend the subjects of general chemistry, such as intramolecular and intermolecular bonds, acidity and basicity, oxidation and reduction and determination of molecular structures, they fail to accurately transfer their knowledge to learning about organic chemistry. In order to promote students' understanding of functional groups and prevent related misconceptions, it is recommended that basic chemistry topics should be reinforced, and the relationship between students' current knowledge and the new information to be learned in organic chemistry should be emphasized with the help of activities in which various forms of thinking are used.