Scopoletin is considered as a marker compound of Morinda citrifolia. Hence, its presence in the fruits of nine different morphotypes of M. citrifolia collected from different locations of South India was investigated. Six different growth stages of the fruit were taken into consideration and qualitative analysis by TLC profiling revealed that scopoletin was present even in the inflorescence stage of the five morphotypes namely, M. citrifolia var. citrifolia BCMML10005, M. citrifolia var. citrifolia BCMML10006, M. citrifolia var. citrifolia BCMML10007, M. citrifolia var. citrifolia BCMML10008 and M. citrifolia var. citrifolia BCMML10009. Interestingly, scopoletin was present in all other fruit stages in all the nine morphotypes. However, quantitative analysis using spectrophotometric assay revealed that scopoletin was present in all the fruit stages of all the nine morphotypes of M. citrifolia.