This study was motivated by the poor performance of students in science (biology) in WAEC and NECO examinations. Research showed that conflicts exist between science and students perceptions of science which results in students developing misconceptions in science, eventually leading to low performance of students in external examinations. As a result, the need to study ecological misconceptions as a major topic in biology syllabus became paramount. The focus of this was to find out the misconceptions held by students in ecology, to determine if sex, cultural background and school type have influence on students conception on ecological concepts. Based on this, four schools were chosen from urban centre and two schools were chosen from the rural location. A total of 246 students participated and two-tier diagnostic questionnaire with 20 items was used as the research instrument. Hypotheses were tested using t-test with 0.05 level of significance. Analysis was done using SPSS and the results showed that students holt much much misconceptions in the tested concepts, and that these misconceptions were not different by sex, but are significantly different by cultural backgrounds and school types with a higher misconceptions existing amongst students in rural and public secondary schools. In sum, improving teaching techniques could ameliorate the challenges inherent with understanding of scientific phenomenon.