Citrus huanglongbing (HLB), caused by phloem-limited ‘Candidatus Liberibacter’ bacteria, is a destructive disease threatening the worldwide citrus industry. The mechanisms of pathogenesis are poorly understood and no efficient strategy is available to control HLB. Chen et al. used a comparative genomics screen to identify candidate microbe-associated molecular patterns (MAMPs) from ‘Ca. Liberibacter’ spp. Their findings identify MAMPs that boost immunity in citrus and could help prevent or reduce HLB infection.