An endophyte Bartalinia pondoensis Marinc of Citrus aurantum L. var. dulcis was isolated and studied for its secondary metabolites and for their Mycobacterium tuberculosis shikimate kinase (MtSK) inhibitory activities. Using LC–MS metabolite fingerprinting of the constituents of the methanol extract, 19 compounds pertaining to various classes were identified: amino acids, proto-alkaloids, fatty acid amides and oxazole, aniline derivatives and aromatic compounds. We report here for the first time the presence of the [N-(ethyloxy, hydroxymethyl)phenylethylamine] as a new proto-alkaloid and 18 other known compounds are reported for the first time in the genus of Bartalinia. MtSK inhibitory activities of methanol extract and fractions obtained by solid phase extraction (SPE) at a concentration of 50 µg/mL may be attributed to the presence of aniline and oxazole derivatives present in all fractions in varying concentrations.