Determining the correct mushroom species with the necessary ecological characteristics is critical to continue mushroom production, which is essential in gastronomy. The mushroom farmers and collectors technique may help identify toxic mushrooms by detecting poisonous mushrooms using images of different mushroom species with distinctive morphological features. However, it can be not easy to distinguish between species. This paper used a dataset of 6714 mushroom images obtained from nine different mushroom species to classify the mushroom species. For a more straightforward comprehension of mushroom images and feature extraction by reanalysis of data sets, data visualization was performed using Grad-CAM, LIME, and Heatmap methods. Residual block-based Convolutional Neural Network (CNN) architectures are trained to automatically classify the concatenated feature map obtained from the Grad-CAM, LIME, and Heatmap methods. After extracting the deep features of the images from each architecture, the Atom Search Optimization (ASO) algorithm has been used to select the most distinctive features. The 6714×9000 size of the concatenated feature map was reduced to 6714×600 using the ASO algorithm. Classification results were evaluated using six different classifiers based on the feature map obtained to determine the mushroom species. The nine classes of mushroom species were classified successfully with 95.45 % accuracy using the proposed model with the ASO algorithm and KNN classifier. The methodology introduces novel visualization techniques for interpreting CNN-based models’ decisions in mushroom species classification tasks. Using metaheuristics-based CNN models with multi-feature fusion techniques allows the model to leverage diverse sources of information, potentially enhancing its ability to discriminate between mushroom species and achieve higher classification accuracy than existing methods. This study can advance the mushroom species classification field by introducing new methodologies, improving classification accuracy, providing insights into model interpretability, and facilitating knowledge transfer to related fields.