In Brazil, the assai (Euterpe oleracea Mart.) is a native palm of the Amazon biome, being exploited in an extractive and predatory way to obtain palm heart and processed pulp. In recent years, there has been an increase in the exploitation of commercial plantations in the country, since extractivism and management of native areas are not able to meet growing demand. In this way, companies of the sector and public institutions have invested in new technologies, such as the improvement of plants, which has increased the demand for good quality seeds, coming from natural ecotypes. Thus, the objective of this work was to evaluate seeds of E. oleracea from three ecotypes regarding the emergence and initial growth of the seedlings in different substrates to guide future plant selection. Seed lots from three assai berry ecotypes were evaluated for water content, seedling emergence, first count, seedling emergence speed index, seedling length and dry mass. The experimental design was completely randomized, with four repetitions of 50 seeds, sown on different substrates. In the physiological characteristics of the seeds and seedlings, there are differences of the three E. oleracea ecotypes. These ecotypes make it possible to identify and select assai palm’s mother plants of Luiz Domingues (IG) and Maracanã (V) natives of areas of the igapó and várzea, respectively, as producers of better quality seeds and seedlings in an alternative substrate (composed of sand, agricultural soil and cattle manure in a proportion of 2:2:1) and, commercial substrate (FORTH® compound of pinus and gray bark), respectively.