This study was aimed at investigating and comparing the microscopy and chemical constituents of the bulbs of Allium cepa L. and Allium sativum L. Comparative analyses including chemo-microscopy, High Performance Liquid Chromatography Analysis (HPLC), and Gas Chromatography–Mass Spectrometry (GC- MS) analyses were carried out. The HPLC analysis for Allium cepa gave 10 peaks and peak number 4 has the highest. While The HPLC analysis for Allium sativum gave 7 peaks and peak number 3 the highest peak, Allium cepa Gas Chromatography-Mass Spectrometry (GC-MS) Analysis showed 47 peaks, corresponding to the name of compounds, while that of Allium sativum Gas Chromatography- Mass Spectrometry (GC-MS) analysis showed 35 peaks as the total number of compounds. Chemo-microscopic analysis of Allium cepa and Allium sativum revealed the presence of lignin, cellulose, tannins, starch, oxalate crystal, oil, protein and absence of mucilage and calcium in the tests carried out. The microscopic characters observed can be used for identification and quality control of the crude drug. The Chromatographic profile of the essential oils of Allium cepa and Allium sativum studied revealed: In Allium cepa, the components with the highest percentage compositions were: Caryophyllene (16.54%), Benzene,1,2,3-trimethyl (6.96%), 3(2H)-Furanone, 2-hexyl-5 methyl (5.73%), Disulphide, dipropyl (5.22%), while the components of Allium sativum with the highest percentage composition were: Diallyl disulphide (40.14%), Benzene,1,2,3-trimethyl (7.02%), Benzene,1ethyl-3-methyl (4.87%), Benzene,1-(bromethyl)-4-(1-methylethy) (4.81%). The results of this research provided information on the essential oil components found in Allium cepa and Allium sativum based on the GCMS analyses. The oils of the two plants find applications in flavorings, fragrances, cosmetics, manufacture of chemicals, pesticides and insecticides as well as being anti-inflammatory, anti-bacterial, anti-fungal agents and anti-infective.