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Reported herein is the synthesis and application of three novel β‐cyclodextrin dimer hosts for the complexation of near infrared (NIR) squaraine dyes in aqueous solution. A series of eight different N‐substituted N‐methyl anilino squaraine dyes with variable terminal groups are investigated, with an optimal n‐hexyl‐substituted squaraine guest demonstrating binding constants orders of magnitude higher than the other squaraine–host combinations and comparable to literature‐reported systems. Moreover, hydrophobic complexation of the squaraine dyes with the β‐cyclodextrin dimer hosts causes drastic changes in the squaraine's photophysical properties, propensity for aggregation and susceptibility to hydrolytic decay.