The research was performed to investigate pollen morphology of endangered species of Capparidaceae in subtropical regions of Pakistan. The distinguishing characters were investigated by using light microscope and scanning electron microscope. Palynological study is comprised of pollen shape, pollen type, exine sculpturing, polar and equatorial diameter, length and width of colpi, mesocolpium, and exine thickness. In polar view, Cleome viscosa exhibited the highest pollen size 26.4 (32.7-24.5 μm) ±0.776 whereas Capparis spinosa appeared to be the lowest 12.6 (14.5-10.7 μm) ±0.400. In equatorial view, Cleome viscosa had the largest pollen size 17.1 (20.0-15.0 μm) ±0.606 and Capparis spinosa had the smallest pollen size 9.7 (12.50-8.00 μm) ±0.394. The maximum fertility percentage has been observed in Capparis spinosa, that is, 98.96% and minimum in Cleome viscosa, that is, 82.93%. Diagnostic key has been constructed to state the essential diagnostic features by means of which the taxa can be identified. Remarkable variations have been observed in pollen size, shape, and exine sculpturing. All the selected species were tricolporate. Prolate to subprolate pollen were observed. There is a great variation existed in exine sculpturing such as in Capparis decidua and C. sp. nova sculpturing is reticulate, in Capparis himalayensis sculpturing is Scabrate granulate, in Capparis spinosa sculpturing is Psilate, in Cleome viscosa sculpturing is regulate-reticulate, in Dipterygium glaucum sculpturing is regulate and in Gynandropsis gynandra sculpturing is striate-regulate. On the basis of overall characteristics of pollen it seems that palynology of this family is helpful at the generic and specific level.