Analogs of marine sponge-derived 3-alkylpyridinium compounds (3-APS) were synthesized and screened for possible antibacterial and antifungal activities. They were found to exhibit moderate antibacterial activity. Antifungal potential was tested on pathogenic fungus Candida albicans, baker's yeast Saccharomyces cerevisiae and hypersaline species Wallemia sebi. S. cerevisiae was the most susceptible to the action of selected 3-APS. Inhibitory effects on fungal growth were also studied on two wood-rotting fungi, brown-rot fungus Gloeophyllum trabeum and a white-rot fungus Trametes versicolor. The former showed a higher susceptibility to the action of 3-APS. The highest antifungal potential was observed with the poly-1,3-dodecyl pyridinium chloride (APS12-3, 7), while a complete loss of activity was noticed with the poly-1,3-butyl pyridinium chloride (APS3, 1), suggesting that this activity may closely correlate to the length of their alkyl chains. Based on our results, synthetic APS12-3 is a good candidate to be used as biocide or wood preservative against wood-rotting fungi.