Volatile compounds have a tremendous impact on fruit quality. We evaluated the volatile compound profiles of ripening wild apple fruit (10 Malus baccata accessions and three Malus prunifolia accessions) in the National Field Genebank for Hardy Fruits at Gongzhuling, China. Alcohols, esters, aldehydes, terpenes, hydrocarbons, ethers, heterocycles, carboxylic acids, and ketones were detected in the M. baccata and M. prunifolia fruit, with the first four being the main volatile compounds present. Of the 92 volatiles detected, esters were the most diverse (49 compounds). This wide range of abundant volatile compounds suggests that M. prunifolia is a good resource for breeding apple cultivars with novel and interesting flavors. The M. baccata accession ‘Zhaai Shandingzi’ and the M. prunifolia accession ‘Bai Haitang’ had the widest range of volatile compounds and the highest volatile compound contents of the accessions examined, and will therefore be good breeding materials for developing commercial lines with enhanced flavor and for widening the genetic diversity. The number of different ester compounds present was significantly positively correlated (r = 0.877) with the cube root of the weight of an individual ripe fruit. Principal component analysis (PCA) showed that the contents of ester compounds could be used to distinguish between M. baccata and M. prunifolia species. Therefore, ester compounds could be used as a reference of parental choice in apple breeding.