Three new borrelidin-type macrolactones, designated as borrelidins JL (4–6), together with borrelidin A (1), borrelidin E (2), and 12-desnitrile-12-carboxyl-borrelidin (3) were isolated from a plant endophytic Streptomyces sp. NA06554. Their structures were determined by extensive spectroscopic analysis including HRESIMS, 1D and 2D NMR data. The antibacterial activities for compounds 1–6 were examined. Borrelidins A (1) and L (6) showed potent and moderate antibacterial activity against Micrococcus luteus, respectively, whereas other derivatives (2–5) are almost inactive, which allows us to propose a plausible structure-activity relationship.