Micellar electrokinetic capillary chromatography (MECC) was developed for the separation of cytokinins including trans-zeatin, trans-zeatin-O-glucoside, dihydrozeatin, dihydrozeatin-O-glucoside, meta-topolin riboside, N6-isopentenyladenine and N6-benzylaminopurine. Under the optimum conditions, i.e. a combination of 10 mM phosphate and 10 mM borate as the running buffer containing 50 mM sodium dodecyl sulphate at pH 10.4, the separation of seven cytokinin standards was accomplished within 11 min. The C18 solid-phase extraction (SPE) method was used to pre-concentrate the putative cytokinins present in the coconut water. Following which, the eluate was further purified using mixed mode Oasis MCX SPE columns and this additional step helps to reduce matrix interference during MECC. After the two solid-phase extraction steps, the optimized MECC method was able to screen for certain cytokinins (zeatin-O-glucoside and dihydrozeatin-O-glucoside) present in coconut water. After this screening, the presence of zeatin-O-glucoside and dihydrozeatin-O-glucoside in coconut water was further confirmed by independent high-performance liquid chromatography and liquid chromatography-mass spectrometry experiments.