Low-molecular weight chitosan-thioglycolic acid has shown significant antibacterial properties against different microorganisms. In order to explore the potential and structure-activity relationships of newly synthesized alkyl thiomers, chitosan has been functionalized with a series of thio-acids with increasing alkyl chain length. All thiomers were characterized with special emphasis on the determination of their degree of deacetylation and substitution, as well as on their molecular weight and amount of thiol groups. The pre-screened chitosan-thiomers were further investigated with plate counting on Pseudomonas aeruginosa, Streptococcus sobrinus and Streptococcus mutans. Furthermore, LIVE/DEAD assays supported the efficiency of chitosan-thiomers against the above microorganisms. All fully characterized chitosan-thiomers showed comparable or enhanced antimicrobial activity compared to pristine chitosan. Our comprehensive approach paves the way to detailed explorations of much sought-after structure activity relationships in the complex chitosan parameter room, starting from correlations between alkyl chain length and antimicrobial activity.