A new method based on partial filling-MEKC (PF-MEKC) directly coupled to ESI-MS was developed for the simultaneous separation and determination of 13 structurally similar cytokinins, including various geometric and positional isomers of cytokinins. On the basis of the resolution of the neighboring isomer peaks, different parameters (i.e., pH and concentration of buffer, surfactant concentrations, length of the injected micellar plug, organic modifier, and applied separation voltage) were optimized to achieve a satisfactory PF-MEKC separation. Under optimum conditions, the separation of 13 cytokinin standards was accomplished within 25 min. MS/MS with multiple reaction monitoring detection was carried out to obtain sufficient selectivity. PF-MEKC-MS/MS allowed for the direct identification and confirmation of the cytokinins present in banana (Musa spp.) pulp sample after extraction and purification. Finally, trans-zeatin riboside (ZR) and trans-zeatin (Z) were unambiguously identified in banana pulp. It is anticipated that the current PF-MEKC-MS method can be applied to analyze cytokinins in a wide range of biological samples.