Study was conducted from April 2011 to May 2012 in Gamo Goffa Zone of Southern Region to characterize indigenous cattle populations and, to identify existing breeding practices and set priority areas of interventions for future genetic improvement for identified cattle populations based on farmer trait preferences. Five sample sites were selected based on the information obtained on the distribution of unique local cattle types. Information were collected through exploratory field visits supported with key informant group discussions, individual farmer interviews using a semi-structured questionnaire, observations and linear body measurements on discrete and continuous variables. Linear measurements were takenfrom 560 mature animals, as were qualitative trait records from 867 animals. General linear model was used to analyze data on reproductive performance, livestock holding and linear body measurement. Tukeys' multiple mean comparison test was employed to compare means offixed effects across sites. Pearson chisquare was used to analyze categorical variables across sites and Borferroni 's correction pair-wise comparisons test was used to check association between categorical variables and sites. Discriminant multivariate analysis was used to separate sample population in to homogenous groups. Mahalanobis' distance measure was employed to find phenotypic distance between sample populations across sites. Nonparametric discriminant analysis was run to look power of categorical variables in discriminating sample population in to similar groups. Findings from the focus group discussion and semi-structured interviews revealed that the indigenous cattle types provide multipurpose and input functions, well adapted to their production environments, and managed under traditional and subsistent mode of production. The most common breeding system in all study sites was pure breeding, although few farmers residing in mid and highland areas exercise crossbreeding. Trypanosomosis, black leg and parasitic diseases were the first three economically important diseases reported by cattle owners. The main selection criteria of breeding animals that owners employ were body size and conformation, milk production, fertility and breeding history of animals. The recalled overall means of reproductive performances were: age at maturity 3.5±0.54 years for males and 4±0.73 years for females, respectively. The overall age at first calving was 4. 95±0. 78 years. Respective culling age of breeding male and female animals was estimated to be 7.11 +2.02 years and 11.8±2.24 years, respectively. The overall productive herd life of cows of 7.96±1.93 years, lifetime calfproduction of 5.64+2.02 calves per cow, calving interval of 1. 77±0.25 years and number of abortions per year per household of 1.13+0.34. The estimated overall mean daily milk yield was 2.27 liters per day. The overall mean milk off-take estimated was 549.45 liter per cow per full lactation and the overall mean lactation length for three lactations estimated was 8.06 months. Prevalence of various cattle diseases, poor infrastructure, limited extension service, and seasonal feed shortage were the most vii common identified constraints of cattle production. On the other hand, available well adaptive local genotype, diversified and suitable agro ecology and high market demand of cattle products are major potential opportunities of cattle production in the study area. Results obtained from analysis of variance on continuous variables showed significant (P<O.OOOl) differences between sites separately for female and male samples. Each of the 14 quantitative traits were highly significant (P<.OOOl). Categorical variables considered were highly significant (p<.0001) between sites. Multiple mean comparisons using Bonferroni's correction and there were strong (P<O.OOOl) associations between discrete variables and sites. Based on discriminant analysis, sample populations were classified into their respective sites with overall hitting rate of 63.15 and 74.89% for females and males, respectively. Canonical discriminant analysis for females and males showed highly significant (P<. 0001) per sites. The Mahalanobis ' distances between sites were also highly significant (P<O.OOOl). Canonical analysis led to identification of two cattle populations that deemed to be distinct breed types (Gamo highland and lowland cattle type). The step-wise discriminant analysis for both male and female sample populations showed that almost all variables had highly significant (p<.0001) power in explaining the phenotypic variation. Therefore, analyses of variance of quantitative variables and qualitative variationsd had classified the sample cattle population of the study sites in to two distinct sub-populations. Thus, indigenous cattle population of the study area was not homogenous based on phenotypic features of qualitative variables and analysis of quantitative traits considered. Some differences in traditional management practices of those two distinct cattle populations had been also observed. Further genetic and confirmatory phenotypic studies should be conducted to generate further information to confirm their separate breed (s). Generally, the current study identified two cattle populations which are different in their phenotypic features. and management practices; and three genetic improvement intervention areas were proposed to improve the productivity of identified cattle population of Gamo Goffa Zone