During the last decade, convolutional neural networks (CNNs) have revolutionised the application of deep learning (DL) methods to classification tasks and object recognition. These procedures can capture key features of image data that are not easily visible to the human eye and use them to classify and predict outcomes with exceptional precision. Here, we show for the first time that CNNs provide highly accurate predictions for small‐scale genetic differentiation and diversity in Ctenomys australis, a subterranean rodent from central Argentina. Using microsatellite genotypes and high‐resolution satellite imagery, we trained a simple CNN to predict local FST and mean allele richness. To identify landscape features with high impact on predicted values, we applied species distribution models to obtain the distribution of suitable habitat. Subsequent use of a machine learning algorithm (random forest) allowed us to identify the attributes that contribute the most to predictions of population genetic metrics. Predictions obtained from the CNN accounted for more than 98% of the variation observed both in FST and mean allele richness values. Random forest regression on landscape metrics indicated that features involving connectivity and consistent prevalence of suitable habitat promoted genetic diversity and reduced genetic differentiation in C. australis. Validation with synthetic data via simulations of genetic differentiation based on the landscape structure of the study area and of a nearby area showed that DL models are able to capture complex relationships between actual data and synthetic data in the same landscape and between synthetic data generated under different landscapes. Our approach represents an objective and powerful approach to landscape genetics because it can extract information from patterns that are not easily identified by humans. Spatial predictions from the CNN may assist in the identification of areas of interest for biodiversity conservation and management of populations.

Understanding the processes and patterns of local adaptation and migration involves an exhaustive knowledge of how landscape features and population distances shape the genetic variation at the geographical level. Ctenomys australis is an endangered subterranean rodent characterized by having a restricted geographic range immerse in a highly fragmented sand dune landscape in the Southeast of Buenos Aires province, Argentina. We use 13 microsatellite loci in a total of 194 individuals from 13 sampling sites to assess the dispersal patterns and population structure in the complete geographic range of this endemic species. Our analyses show that populations are highly structured with low rates of gene flow among them. Genetic differentiation among sampling sites was consistent with an isolation by distance pattern, however, an important fraction of the population differentiation was explained by natural barriers such as rivers and streams. Although the individuals were sampled at locations distanced from each other, we also use some landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. These analyses showed that the sand dune habitat availability (the most suitable habitat for the occupation of the species), was one of the main factors that explained the differentiation patterns of the different sampling sites located on both sides of the Quequén Salado River. Finally, habitat availability was directly associated with the width of the sand dune landscape in the Southeast of Buenos Aires province, finding the greatest genetic differentiation among the populations of the Northeast, where this landscape is narrower.