The main objective of the study was to determine Pre-service Chemistry Teachers’ (PCTs) understanding of isomerism related concepts of Aliphatic Hydrocarbons (AHs). To get in-depth picture of PCTs understanding on isomerism related concepts of AHs, case study was employed. The sample for this study consisted of twelve participants selected from 87 PCTs randomly, in two classes. These were second year PCTs registered in Introductory Organic Chemistry I course in Arbaminch College of Teachers Education, Southern, Nations, Nationalities and Peoples Regional State (SNNPRS), Ethiopia in the year 2017 G.C. A semi-structured interview was used for judging understanding of PCTs in relation to isomerism concepts. A framework analysis approach was applied to analyze interview data. The results of analysis revealed that the PCTs in the Intervention Group (IG) had better acquisition of isomerism concepts than those in the Comparison Group (CG). Based on the results and discussions, conclusions were made.