Garlic is one of the most important crops in Brazil and in the world. In Piaui State, specifically in micro region of Picos, semi-noble garlic was once grown on a large scale and supplied the demand of various municipalities in the state. After the noble garlic was introduced to the Brazilian market, the production of semi-noble garlic reduced which may have led to loss of genetic diversity. This study investigated the genetic diversity in twelve varieties of garlic, four originally from Piaui State and eight from the Garlic Germplasm Collection of the College of Agricultura "Luiz de Queiroz"--Universidade de Sao Paulo (ESALQ / USP). The present study characterized the germplasm based on descriptions proposed by the International Plant Genetic Resources Institute (IPGRI), currently Bioversity International, and conducted the genotyping of varieties from eight SSR loci. The agronomic characters and microsatellite genotyping were efficient to estimate genetic diversity among the garlic varieties. The results obtained with the morphological analysis corroborated the molecular analyses, demonstrating complementarity of these analyses dimensions in the study of genetic diversity in garlic. Thus, we concluded that genetic diversity exists among the varieties of garlic studied in terms of the germplasm origin and suggests that the material from the ESALQ / USP is a germplasm distinct from that grown in Piaui State. The genetic divergence among varieties of garlic in Piaui State indicates the possibility of selecting superior genotypes that increase the competitiveness of garlic from Piaui State against imported garlic.