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Pure methoxyfuranocoumarins were isolated from a crude petroleum ether extract (CPE; Soxleth extraction efficiency 12.28%) from fruits of Peucedanum tauricum MB. (Apiaceae) by counter-current chromatography in a hydrostatic equilibrium system (centrifugal partition chromatography—CPC). The optimized biphasic solvent system composed of n-heptane-ethyl acetate-methanol-water (5:2:5:2; v/v/v/v) in the ascending mode of elution was used (3 mL/min, 1600 rpm). In the single run, peucedanin (P), 8-methoxypeucedanin (8MP), and bergapten (5MOP) were obtained as pure as 95.6%, 98.1%, and c.a. 100%, respectively. The carefully optimized and developed CPC was effectively transferred from the analytical to the semi-preparative scale (where 20 mg and 150 mg of CPE were loaded, respectively). Identification and quantitative analysis of methoxyfuranocoumarins was carried out in the plant material, in the CPE, and in individual CPC fractions by use of validated high-performance liquid chromatography with diode array detection and mass spectrometry (HPLC-DAD-ESI-MS). For the separation steps, the extraction/isolation recovery was calculated. In this case, CPC proved to be an effective tool for the simultaneous isolation and separation of P, 8MP, and 5MOP from a multicomponent plant matrix, without additional pre-purification steps. The high purity of the obtained plant metabolites makes it possible to consider their use in pharmacological or biological studies.