A well-characterized germplasm is a requisite to develop productive and better adapted crop cultivars. Morphological and molecular markers and pedigree analyses are widely used in germplasm characterization, and to establish genetic diversity and relationship in maize. The objectives of this study were to characterise newly developed quality protein maize (QPM) inbred lines adapted to tropical-highlands using phenotypic traits and to determine the association with simple sequence repeat (SSR) markers. Thirty-six maize inbred lines (30 QPM and six non-QPM) adapted to tropical-highlands of Ethiopia were evaluated using 18 phenotypic traits and 26 selected SSR markers. Significant phenotypic variations were observed among inbred lines for all measured traits. Grain yield showed moderate and high genotypic and phenotypic coefficients of variation, respectively. Ear height and thousand kernel weight had high heritability (≥ 0.70) which could be a source of high genetic advance through selection. Principal component and cluster analysis using unweighted paired group method using arithmetic averages (UPGMA) revealed the presence of two to four distinct genetic groups, while population structure analysis based on phenotypic data showed the presence of four to six genetic groups. Seven QPM inbred lines (KIT32Q, 142-1eQ, SRSYN20Q, FS67(BC 2 ), FS170Q, FS60, and F7215) with complementary phenotypic traits and relatively better yield performance were selected using the phenotypic traits and SSR based genotyping for cultivar development and/or conservation.