The prediction of imminent bankruptcy for a company is important to banks, government agencies, business owners, and different business stakeholders. Bankruptcy is influenced by many global and local aspects, so it can hardly be anticipated without deeper analysis and economic modeling knowledge. To make this problem even more challenging, the available bankruptcy datasets are usually imbalanced since even in times of financial crisis, bankrupt companies constitute only a fraction of all operating businesses. In this article, we propose a novel bankruptcy prediction approach based on a shallow autoencoder ensemble that is optimized by a genetic algorithm. The goal of the autoencoders is to learn the distribution of the majority class: going concern businesses. Then, the bankrupt companies are represented by higher autoencoder reconstruction errors. The choice of the optimal threshold value for the reconstruction error, which is used to differentiate between bankrupt and nonbankrupt companies, is crucial and determines the final classification decision. In our approach, the threshold for each autoencoder is determined by a genetic algorithm. We evaluate the proposed method on four different datasets containing small and medium-sized enterprises. The results show that the autoencoder ensemble is able to identify bankrupt companies with geometric mean scores ranging from 71% to 93.7%, (depending on the industry and evaluation year).