Thymus marschallianus Willd. is a Lamiaceae species spread in a large variety of habitats worldwide. The aim of the present research was to analyse two different samples belonging to this species, one obtained from the spontaneous flora and one from culture. The total polyphenols, flavonoids, and phenolic acid contents were spectrophotometrically determined. Qualitative and quantitative analysis of polyphenols was performed by an HPLC-DAD-ESI (+)-MS method. For the antibacterial assay, the well-diffusion and the broth microdilution methods were used. Analysis of polyphenols revealed for both samples the presence of flavonoids like luteolin, quercetin, apigenin and their derivatives, but also of rosmarinic acid and methyl-rosmarinate. Differences regarding the amount of these compounds were emphasized. Significantly larger amounts of flavonoids were found for the sample harvested in the spontaneous flora, while for the rosmarinic acid, larger amounts were found for the cultured sample. Both samples displayed promising antibacterial activity, particularly towards Gram positive organisms. T. marschallianus represents, therefore, a rich source of polyphenolic compounds that prove its promising potential as a medicinal species.