Carbazole alkaloids induce apoptosis in HL-60 cells through activation of the caspase-9/caspase-3 pathway and they are targeted as potential anticancer agents. Thus, the naturally occurring carbazole alkaloids become important as precursors for lead optimization in drug development. A method based on ultra performance liquid chromatography coupled with photodiode-array detection was developed using reverse phase isocratic elution with 85:15 acetonitrile and ammonium acetate buffer (5 mM). Seven samples of Murrya koenigii (L.) Spreng. from north-central India (Uttar Pradesh) were analyzed. All three targeted analytes, koenimbidine (mk1), koenimbine (mk2) and mahanimbine (mk3), were well separated within 4.0 min with linearity of the calibration curves (r2 > 0.999). The limits of detection and quantification of mk1, mk2 and mk3 were 0.7, 0.4, 0.04 μg/mL and 2.14, 1.21, 0.12 μg/mL, respectively. The natural abundance of mk1, mk2 and mk3 was 0.06-0.20, 0.04-0.69 and 0.13-0.42%, w/w, respectively, in the dried powdered leaves, whereas, the tissue specific distribution of carbazole alkaloids was observed in the order of predominance, mk1 leaf>root>fruit>stem, mk2 fruit>leaf >stem>root, and mk3 fruit>leaf>root>stem. The developed method was validated for limits of detection and quantification, repeatability, accuracy, precision and stability. This is the first report on the natural abundance of the major carbazole alkaloids in M. koenigii and the method developed can be used in HPLC/UPLC systems.