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A new family of squaramide-based anionophores (L1–L8) have been synthesised and fully characterised with the aim to investigate the effect of indolyl substituents on their anion binding and transmembrane transport properties. L1, L2, L6, and L8, bearing a 7-indolyl/indol-7-yl moiety as the substituent, were found to be the most efficient of the series in binding chloride with high stability constants. L1, L6, and L8 were also found to be the most potent anionophores of the series, able to mediate transmembrane anion transport. In particular, L6 bearing the 3,5-bis(trifluoromethyl)phenyl group was found to be the most active transporter, and its efficiency as an anionophore/anion transporter was favourably compared with that of their symmetrically-substituted squaramide analogues L9 and L10, previously reported in the literature., Consejería de Educación de la Junta de Castilla y León (project BU067P20) and the Ministerio de Ciencia e Innovación (project PID2020-117610RB-I00). I. C.-B. and D. A.-C. thank the Consejería de Educación de la Junta de Castilla y León, the European Social Fund (ESF) and the European Regional Development Fund (ERDF) for their post-doctoral (I. C.-B.) and pre-doctoral (D. A.-C.) contracts. The authors gratefully acknowledge Andrea Sancho-Medina for her contributions to transmembrane anion transport experiments. Financial support from MIUR (PRIN 2017 project 2017EKCS35) is gratefully acknowledged by C. C. and G. P. along with the Università degli Studi di Cagliari (FIR 2016-2019) and the Fondazione di Sardegna (FdS Progetti Biennali di Ateneo, annualità 2020, project F75F21001260007).