Flow (FCM) and image cytometry (ICM) and 18S-25S ribosomal DNA (rDNA) fluorescence in situ hybridisation (FISH) were used to analyse the genetic stability or variation in oil palm in vitro plantlets, various forms of calli, and slow- and fast-growing liquid suspension cultures. Both FCM and ICM results show a similar correlation pattern where samples with lower DNA content had lower integrative optical density (IOD) peaks. The 18S-25S rDNA FISH showed two large signals in the interphase cells of calli analysed, indicating a diploid ploidy level. Significant differences were observed in the DNA content and pattern of nuclei activity of the slow- and fast-growing liquid suspension cultures using FCM and ICM analysis, demonstrating the usefulness of the above-mentioned tools developed to analyse materials prior to micropropagation; hence, the oil palm’s clonal fidelity is ensured, and the efficiency and robustness of liquid culture are improved by selecting callus materials which have similar DNA content and IOD range and peak as the fast-growing friable suspension and friable calli used in this study.