Malusplants are frequently devastated by the apple rust caused byGymnosporangium yamadaeMiyabe. When rust occurs, mostMalusspp. and cultivars produce yellow spots, which are more severe, whereas a few cultivars accumulate anthocyanins around rust spots, forming red spots that inhibit the expansion of the affected area and might confer rust resistance. Inoculation experiments showed thatMalusspp. with red spots had a significantly lower rust severity. Compared withM. micromalus,M.‘Profusion’, with red spots, accumulated more anthocyanins. Anthocyanins exhibited concentration-dependent antifungal activity againstG. yamadaeby inhibiting teliospores germination. Morphological observations and the leakage of teliospores intracellular contents evidenced that anthocyanins destroyed cell integrity. Transcriptome data of anthocyanins-treated teliospores showed that differentially expressed genes were enriched in cell wall and membrane metabolism-related pathways. Obvious cell atrophy in periodical cells and aeciospores was observed at the rust spots ofM.‘Profusion’. Moreover,WSC,RLM1, andPMA1in the cell wall and membrane metabolic pathways were progressively downregulated with increasing anthocyanins content, both in thein vitrotreatment and inMalusspp. Our results suggest that anthocyanins play an anti-rust role by downregulating the expression ofWSC,RLM1, andPMA1to destroy the cell integrity ofG. yamadae.