Knowledge of the genetic variation of crop collections is essential for their efficient use in plant breeding programs. The Ethiopian Highland Maize Germplasm Collection Mission was launched throughout the highlands of Ethiopia in 1998 and 287 traditional maize accessions were collected from farmers’ fields. To date, no information was available on the morphological and genetic diversity in this important collection. Various molecular marker techniques and quantitative genetics approaches were applied to accurately unravel the extent of phenotypic and genetic diversity, to study patterns of morphological and molecular variation and to determine association of molecular markers with quantitative trait variation, with the view of designing a sound breeding program and management strategy for maize in the highlands of Ethiopia. The morphological study confirmed that traditional Ethiopian highland maize accessions contain large amounts of variation for agro-morphological traits. The broad trait diversity observed among the accessions suggested ample opportunities for the genetic improvement of the crop through selection directly from the accessions and/ or the development of inbred lines for a future hybrid program. Selection practices followed by local farmers are mostly consistent within agroecology and gave rise to morphologically distinct maize accessions in different agroecologies. This underscores the importance of considering farmers’ knowledge of diversity in the collection and evaluation of local accessions. The results of amplified fragment length polymorphism (AFLP) and microsatellite or simple sequence repeat (SSR) marker analyses showed that bulking leaf samples from 15 individual plants per out-bred accession is an effective means of producing representative profiles of individual plants, thereby reducing the cost of DNA extraction and subsequent marker analysis of open-pollinated varieties. Cluster analyses based on AFLP and SSR data showed that most of the accessions collected from the Northern agroecology were genetically distinct from the Western and Southern accessions suggesting that differentiation for adaptive traits for drought conditions may have occurred in the Northern accessions. However, there was very little genetic differentiation between the Western and Southern accessions suggesting gene flow between the two agroecologies and recent introduction of similar improved varieties in these agroecoogies . In both marker systems, high mean genetic diversity was observed among the traditional Ethiopian highland maize accessions. This is possibly due to (i) the continuous introduction of maize from abroad by different organizations; (ii) genetic variation generated through farmers management practices; and (iii) the presence of different environmental conditions in the highlands of Ethiopia to which local landraces may have been adapted. The correlation between the morphological dissimilarity matrix and the matrices of genetic dissimilarity based on SSR and AFLP markers were 0.43 and 0.39, respectively (p = 0.001 in both cases). The correlation between SSR and AFLP dissimilarity matrices was 0.67 (p = 0.001). These significant correlations indicate that the three independent sets of data likely reflect the same pattern of genetic diversity, and validate the use of the data to calculate the different diversity statistics for Ethiopian highland maize accessions. From this study, three groups of maize accessions with distinctive genetic profiles and morphological traits were identified that will be useful for future collection, conservation and breeding programs of maize for the highlands of Ethiopia. A pilot association study using SSR markers and quantitative trait variation indicated that molecular markers could be useful to identify genetic factors controlling earliness, tallness, grain yield and associated traits, which could be exploited by various breeding schemes. The analytical tools outlined in this dissertation can be a useful tool in managing genetic variation of open-pollinated crops and will aid in the conservation of unique genetic diversity. Production stability and global food security are linked to the conservation and exploitation of worldwide genetic resources and this research attempts to add to that body of knowledge. Copyright 2005, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Beyene, YA 2005, Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays l.) using molecular markers and morphological traits : implication for breeding and conservation, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-02212006-112610 / > / Thesis (PhD (Genetics))--University of Pretoria, 2005. / Genetics / unrestricted