Ethiopia is one of the sub-Saharan African countries with alarming population growth rate and high total fertility rate. To reduce high population growth and high fertility, the usage of modern contraceptive methods which classified as short term and long term methods is crucial among women. Despite widespread adoption of family planning in the developing world, the usage of modern contraceptive methods and preference of long term method is still relatively very low in sub-Saharan Africa including Ethiopia. Hence, the general objective of this study was assessing the prevalence of modern contraceptive methods and identifying the potential factors influencing the preferences of long term contraceptive methods among married women of reproductive age in Arba Minch town. Community based cross sectional study design was employed. A single stage simple random sampling was used as sampling technique and sample of 990 women was determined using a formula for estimation of single population proportion. Descriptive analysis was employed to estimate the prevalence and potential predictors were selected by using chi-square test of association between preference of the modern contraceptive methods and predictors. Those predictors that showed p-value less than or equal to 0.25 were taken to binary logistic regression analysis to identify the determinants. From a descriptive analysis, out of 990 sampled married women about 57.9% (573) were modern contraception methods users. Among these 573 modern contraceptive method users, 147 (27.73%) were long term methods users, like injectable, implant and intrauterine devices. From binary logistic regression analysis, age of the respondent, religion of women, number of children in a family, education level of women, desire for more child, experience on modern contraceptive use, frequency of watching television, availability of service in nearby place and service provider were found to be statistically significant predictors of preference of long term contraceptive methods among married women of reproductive age in Arba Minch town.