In the present era, environmental glitches associated with extensive emission of greenhouse gases (GHG) and energy crises caused by exhausting fossil fuel reservoirs has diverted researcher's interest toward alternative and renewable energy sources. Biodiesel is a renewable, biodegradable, and sustainable alternative to petro‐diesel. Biodiesel synthesized from non‐edible seed oils is preferred due its cost effectiveness and eco‐friendly nature. Hence, our present study focused on investigation and identification of micromorphological characters of six novel, non‐edible seed oil feedstock for biodiesel production via scanning electron microscopy (SEM). Results of light microscopy of seeds revealed distinct variation in seed size (15.8–1.8 mm in length and 9.4–1.1 in width), shape (round to Cuneiform), and color (from black to yellowish green). Non‐edible seed oil content fall in range of 28–38% (wt/wt). Free fatty acid (FFA) content varied from 0.56 to 2.06 mg KOH/g. Multivariate analysis was performed to investigate correlation between three significant variables of seed oil yielding feedstock such as potential for biodiesel synthesis, oil content, and FFA content via principal component analysis. Ultra morphological investigation of seeds surfaces via SEM exhibited distinctive variation in surface sculpturing, cell arrangement, cell shape, periclinal wall shape, margins, protuberances, and anticlinal wall shape. Seed surface sculpturing varied from reticulate, semitectate, wrinkled, rugose, papillate, perforate, and striate. Periclinal wall arrangements confirmed variation from glabrous, raised, depressed, elevated, smooth, pentagonal, entire, and ripple margins. Whereas, anticlinal walls pattern demonstrated variation from angular, smooth, wavy, deep, dentate, entire, irregular, puzzled, elongated, curved, and depressed. Finally, it was concluded from obtained results that SEM could be a possible useful tool in disclosing veiled micromorphological characters of non‐edible oil yielding seeds, which provides useful information to researchers for their correct, authentic identification, and classification in modern synthetic system.