Summary Hibiscus cannabinus var. HC-2 (2nϭ2xϭ36) and H. sabdariffa var. HS-24 (2nϭ4xϭ72) were cytogenetically and biochemically studied to elucidate their genomic homology. Both the species possessed only metacentric chromosomes. The range of chromosome length of these 2 species was 1.43-3.80 mm. Both the species showed a gradual decrease in chromosome length. Six CMA-positive bands were found in both the species. Two entirely CMA-positive banded chromosomes were found in both the species. Twenty six DAPI-positive bands were found in H. cannabinus var. HC-2. In H. sabdariffa var. HS-24, 14 DAPI-positive bands appeared. These bands were distributed in different location of respective chromosomes. Two chromosomes of H. cannabinus var. HC-2 and 8 chromosomes of H. sabdariffa var. HS-24 were entirely banded with DAPI. The entirely CMA-and DAPI-banded chromosomes were unique and could be used as marker. In H. cannabinus var. HC-2, a pair of satellites was found in orcein and CMA-staining. No satellite was found in DAPI-staining indicates its GC-rich nature. The activity of acid phosphatase and peroxidase was found similar in both the species. However, the 2 species showed different activities for esterase. The karyotypes (conventional and fluorescent) and electrophoresis pattern (acid phosphatase and peroxidase) indicates that either out of 2 different genomes in H. sabdariffa var. HS-24, 1 is very close to that of H. cannabinus var. HC-2 or H. sabdariffa var. HS-24 and H. cannabinus var. HC-2 may have derived their part of genomes from a common ancestor.