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The properties of phosphonium polyelectrolytes (PELs) were evaluated in an effort to assess the influence of both side chain and main chain composition. The influence of side chain was examined by comparing properties of a series of PELs having hydrophobic octyloxy side chains to those of structural analogues lacking the side chains. The influence exerted by backbone flexibility/length of spacer between charges was revealed by comparing properties of two series of polymers with a variable number of methylene units between phosphonium charge‐bearing sites. Side chain composition and spacing between phosphonium units lead to noteworthy influence on thermal stability, glass transition, and crystallinity. The molecular structure of PELs also correlates with trends in film morphology and critical surface energy of PEL dip‐cast films. Sensitivity of morphology to humidity or water in the casting solvent was observed. Supramolecular assembly of films via layer‐by‐layer deposition of PELs alternating with anionic polythiophene derivative layers was also undertaken. The linearity of film growth, amount of material deposited in each bilayer, polycation:polyanion ratio, and film roughness all show noteworthy trends that depend on both the presence/absence of side chains and on spacing between ionic centers. The relationship between side chain and spacer on bactericidal activity againstStaphylococcus aureusandEscherichia coliwas assessed. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem.2019, 57, 24–34