Gymnosporangium species (Pucciniaceae, Pucciniales, Basidiomycota) are the causal agents of cedar-apple rust diseases, which can lead to significant economic losses to apple cultivars. Currently, the genus contains 17 described species that alternate between spermogonial/aecial stages on Malus species and telial stages on Juniperus or Chamaecyparis species, although these have yet to receive a modern systematic treatment. Furthermore, prior studies have shown that Gymnosporangium does not belong to the Pucciniaceae sensu stricto (s.str.), nor is it allied to any currently defined rust family. In this study we examine the phylogenetic placement of the genus Gymnosporangium. We also delineate interspecific boundaries of the Gymnosporangium species on Malus based on phylogenies inferred from concatenated data of rDNA SSU, ITS and LSU and the holomorphic morphology of the entire life cycle. Based on these results, we propose a new family, Gymnosporangiaceae, to accommodate the genus Gymnosporangium, and recognize 22 Gymnosporangium species parasitic on Malus species, of which G. lachrymiforme, G. shennongjiaense, G. spinulosum, G. tiankengense and G. kanas are new. Typification of G. asiaticum, G. fenzelianum, G. juniperi-virginianae, G. libocedri, G. nelsonii, G. nidus-avis and G. yamadae are proposed to stabilize the use of names. Morphological and molecular data from type materials of 14 Gymnosporangium species are provided. Finally, morphological characteristics, host alternation and geographical distribution data are provided for each Gymnosporangium species on Malus.