Understanding pupils’ biodiversity perspectives is essential to developing educators’ sensitivity to students’ multi-faceted views of the world, thus increasing teaching effectiveness. In this study, we asked 1528 school pupils in the Azores to choose between alternative schemes in three ecological scenarios and to justify their decisions. The study’s objectives were to understand biodiversity perspectives underlying pupils’ choice of the most desirable schemes for nature and to examine whether gender and school level (middle school/high school) influenced their choices. Quantitative (frequency analysis and Chi-square statistics) and qualitative (thematic analysis) methods were applied for data analysis. The majority of pupils made appropriate choices, arguing from different biodiversity perspectives, which were classified in 10 categories and 24 subcategories. High school pupils did not exhibit significant differences among the main arguments employed, and mostly referred to ecological concepts, while middle school pupils exhibited different choices according to gender, emphasizing richness over the threats posed by introduced species. Biodiversity education should thus be strengthened, especially at the middle school level, where different complex issues would benefit from classroom discussion and systematization. The chosen methodological strategy proved to be effective in assessing pupils’ biodiversity perspectives, which may be useful to deal with other ill-structured problems.