Camu-camu (Myrciaria dubia), a fruit from the Amazon region, has received attention due to its high content of antioxidant compounds such as ascorbic acid and polyphenols. This study’s objective was to select camu-camu clones according to their morphological characteristics using multivariate analyses. We evaluated 56 camu-camu clones distributed in three blocks with two plants per experimental plot. The variables measured were plant height (H), number of basal branches (NBB), number of terminal buds (NTB), basal stem diameter (BSD), chlorophylls a (Chl a) and b (Chl b), and total chlorophyll (Chl a + b). Principal component (PCA) and multivariate clustering analyses were performed using the average linkage mean and Mahalanobis distance algorithms. After 24 months, results showed that the characteristics that least contributed to clone selection was NBB. The plant height (H), number of terminal buds (NTB), basal stem diameter (BSD), chlorophylls a (Chl a) and b (Chl b), and total chlorophyll (Chl a + b) had the most positive contribution towards the initial selection of camu-camu clones at two years of age. The 22 camu-camu clones showed the highest rate of vegetative development or vegetative quality index (VQI) in the transitional savanna/forest area of the northern Amazon, Brazil, after two years of transplanting.