Background: Coleus forskohlii is a well-known industrially important medicinal plant, for its high forskolin content. Objective: A simple, selective, and sensitive high-performance thin layer chromatography (HPTLC) method was developed and validated for simultaneous quantification of forskolin and iso-forskolin in C. forskohlii germplasm collected from the Eastern Ghats, India. Materials and Methods: Chromatographic separation of the targeted marker(s) was obtained on precoated silica plates using toluene: ethyl acetate: methanol (90:30:0.5, v/v/v) as the mobile phase. Results: Densitometric quantification of forskolin and iso-forskolin was carried out at 545 nm. Forskolin and iso-forskolin were identified by comparing the ultraviolet spectra of standard and sample track at Rfof 0.64 ± 0.02 and 0.36 ± 0.01, after derivatization with anisaldehyde sulfuric acid reagent. The linearity of both the analytes was obtained in the range of 300–1200 ng/spot with the regression coefficient (R2) of 0.991 and 0.986. Recovery of analyte (s) at three levels, namely, 100, 150, and 200 ng/spot was found to be 100.46% ± 0.29%, 99.64% ± 0.33%, 100.02% ± 0.76% and 99.76% ± 0.62%, 99.56% ± 0.35%, 100.02% ± 0.22%, respectively, for forskolin and iso-forskolin. The content of forskolin and iso-forskolin varies from 0.046% to 0.187% and 0.002% to 0.077%, respectively (dry weight basis), the maximum content of both the markers was found in NBC-31, from Thakurwada, Maharashtra. Conclusion: The developed HPTLC method was linear, accurate, and reliable as per the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use guidelines. The study aids in the identification of elite chemotype for commercial prospection of industrially viable medicinal crop.