In this study, concept maps and mind maps, which are alternative assessment and evaluation tools used in science education, were examined. The study aimed to quantitatively evaluate the concept maps and mind maps prepared by pre-service science teachers dealing with the concept of atoms. Thus, it was aimed to describe the concept of atom in the minds of pre-service teachers with different assessment tools. A case study approach was used in the study, which is one of the quantitative research designs. The study group consisted of 15 pre-service teachers teaching science in the fourth grade. Criterion sampling method was used in the study. Attention was paid to ensure that the participating pre-service teachers had undertaken all the relevant courses regarding the subject of atoms. The concept maps and mind maps created by the participants were used to describe their cognitive structures about the atom concept. The concept maps and mind maps created by the preservice teachers were examined using quantitative analysis. It was concluded that the scores obtained by the pre-service teachers from both the alternative assessment and evaluation tools were close to their total mean scores. It was determined that the pre-service teachers could not advance as the structure grew in both concept maps and mind maps, and they had difficulties in establishing relationships between levels and hierarchies.