Strawberry can be categorized into seasonal-flowering(SF) and perpetual-flowering(PF) depending on their flowering habit. To understand the molecular mechanisms underlying the two flowering pattern, a comparative proteomic analysis of the shoot apical meristem(SAM) was performed between the PF cultivar 'Monterey' and the SF cultivar 'Benihoppe'. 1088 differentially expressed proteins (DEPs) between the two cultivars were identified, of which 536 were up -regulated and 552 down-regulated in 'Monterey'. Gene Ontology analysis revealed DEPs were enriched in biological processes related to flavonoid metabolism, pigment metabolism, response to stimuli, circadian rhythm, developmental growth involved in morphogenesis, reproductive structure development and etc.. KEGG analysis indicated that DEPs were involved in several metabolic pathways, including flavonoid biosynth esis and amino acid metabolism. Protein-protein interaction analysis showed flowering related DEPs SPL3, TFL1, ELF4, HDA6, COI1 formed two interacting network. Our findings provide proteomic data for understanding the molecular basis of SAM development during the transition from vegetative to reproductive growth in strawberry.