Wildland conservation efforts require accurate maps of plant species distribution across large spatial scales. High-resolution species mapping is difficult in diverse, dense plant communities, where extensive ground-based surveys are labor-intensive and risk damaging sensitive flora. High-resolution satellite imagery is available at scales needed for plant community conservation across large areas, but can be cost prohibitive and lack resolution to identify species. Deep learning analysis of drone-based imagery can aid in accurate classification of plant species in these communities across large regions. This study assessed whether drone-based imagery and deep learning modeling approaches could be used to map species in complex chaparral, coastal sage scrub, and oak woodland communities. We tested the effectiveness of random forest, support vector machine, and convolutional neural network (CNN) coupled with object-based image analysis (OBIA) for mapping in diverse shrublands. Our CNN + OBIA approach outperformed random forest and support vector machine methods to accurately identify tree and shrub species, vegetation gaps, and communities, even distinguishing two congeneric shrub species with similar morphological characteristics. Similar accuracies were attained when applied to neighboring sites. This work is key to the accurate species identification and large scale mapping needed for conservation research and monitoring in chaparral and other wildland plant communities. Uncertainty in model application is associated with less common species and intermixed canopies.