Flying fishes are typical marine pelagic fishes (Beloniformes: Exocoetidae) occurring in tropical and subtropical regions. They are described in six genera, among which Cheilopogon is the widely distributed genus, with four species occurring in Indian waters. The present communication describes the pigmentation variations in manyspotted flying fish, Cheilopogon spilopterus (Valenciennes, 1847), collected from India's East and West coasts. The colour variations, morphology and chances of phenotypic plasticity recorded in the C. spilopterus are described herewith, along with a comparative account of morphometric and molecular traits of variants and normal individuals. No significant difference in morphology was found between the normal and variant specimens of C. spilopterus from the East and West coasts. However, there are visible clear spot pattern variations in the paired fins from the East coast to the West coast. The genetic distances between the normal and variant specimens are as low as 0 and 0.0036 for the mitochondrial COI gene, which confirms that all the specimens are of C. spilopterus and the interspecific divergence is more than 0.01. The prominent variations in spot patterns may be due to environmental attributes.