Marine cyanobacteria, such as Synechococcus are among the most abundant and widespread primary producers in the open ocean. Synechococcus strains belonging to different clades have adapted distinct strategies for survival across a range of marine niches: from turbid, estuarine waters to transparent oligotrophic waters and various temperatures across 1200 of latitude. Clades I and IV are prevalent in colder, mesotrophic, coastal waters, while clades II and III show preference for the warmer, oligotrophic open oceans. To gain insight into the relative resources these unicellular organisms invest into adaptation strategies we performed shotgun proteomics, focusing on the membrane proteomes, of four Synechococcus spp. strains namely CC9311 (clade I), CC9605 (clade II), WH8102 (clade III) and CC9902 (clade IV). More than 600 distinct proteins were identified in membrane extracts of each species and their relative expression levels were determined using label-free quantification. Membrane transporter systems were abundant in all strains, with 63-92 membrane transport proteins identified and accounted for 8-17% of overall proteins expression. Comparative membrane proteome analysis showed that CC9902 and WH8102 have a significant resource investment in phosphate uptake, which represent 44% and 38% of its own overall transporter protein expression. WH8102 displayed high expression of the FutA (iron ABC transporter substrate binding protein) suggested that high binding affinity of iron is a key adaptation strategy in oligotrophic environments. One protein annotated as a phosphatase 2C enzyme was very highly expressed in the temperate/coastal strains CC9311 and CC9902, suggested this protein serves a vital, but yet undefined function, for strains living in these environments. Overall, this study suggested that membrane transporters and sensing systems are key components in the different adaptation strategies of cyanobacteria.