Melissa officinalis L. is an aromatic and perennial bushy plant with interesting pharmacological and biological properties, which extensively distributed in the Mediterranean region and Asia. In order to domestication and breeding of this plant, an assessment of phytochemical and morphological diversity among 65 individuals of 7 wild and 6 agro-ecotypic populations at full flowering stage, collected from 5 northern provinces of Iran, was carried out on the basis of morphological and phytochemical traits. The average of essential oil content was 0.13% to 0.35% (w/w). The characterization of the essential oils by gas chromatography-flame ionization detector (GC-FID) and gas chromatography–mass spectrometry (GC/MS) analyses revealed that all 65 sampled individuals were divided into the 3 chemotypes; chemotype I (geraniol and limonene-10-ol), chemotype II (geranyl linalool and thymol), and chmotype III(caryophyllene oxide and bergamotolacetet), which are comprising 10, 1, and 2 accessions, respectively. The major constituents in all 13 accessions essential oil were limonene-10-ol, geraniol, and caryophyllene oxide. The number of lateral branches, the length of petiole, and the length of lateral stem (CVs of 34.07, 26.28, and 22.82%, respectively) were the main morphological features with high variability among the other studied populations. The high chemical differentiation among and within populations based on their geographical and bioclimatic distribution enforces a breeding approach to gain homogenous cultivars suitable for the agriculture and industry.