Over the past three centuries, maize has become adapted to complex environmental conditions in the
highlands of Ethiopia. We analyzed 62 traditional Ethiopian highland maize accessions, using 20 simple
sequence repeat (SSR) markers and 15 morphological traits, to assess genetic diversity and relationships
among these accessions and to assess the level of correlation between phenotypic and genetic distances. The
accessions varied significantly for all of the measured morphological traits. The average number of alleles
per locus was 4.9. Pair-wise genetic dissimilarity coefficients ranged from 0.27 to 0.63 with a mean of 0.49.
Ward minimum variance cluster analysis showed that accessions collected from the Northern agroecology
were distinct from the Western and Southern agroecologies. However, there was no differentiation between
the Western and Southern accessions. This suggested gene flow between these regions. The relationship
between morphological and SSR-based distances was significant and positive (r = 0.43, p = 0.001). The
high genetic diversity observed among these set of accessions, suggests ample opportunity for the development
of improved varieties for different agroecologies of Ethiopia. From conservation perspective,
sampling many accessions from all agroecologies would be an effective way of capturing genetic variation
for future collections and conservation.