During the last decade, the worldwide market for fresh citrus fruits, mainly those that are seedless with easy-peeling and nice orange-colored skin, greatly increased. The elaboration of organoleptic quality is strongly defined by genetic and environmental components and their interaction. While several mandarin breeding programs have been developed worldwide, very few focus on the issues of tropical areas, and few data are available for citrus germplasm evaluation in a tropical environment. To optimize the mandarin production system, research related to the exploration of existing citrus germplasm, the expansion of the genetic base of orchards and the evaluation of the agronomic potential of new genotypes must be conducted. The objective of this study was to characterize and evaluate 25 mandarin varieties from typical Brazilian tropical citrus germplasm according to genetic, morphological and physicochemical traits over two consecutive years. Simple correlation coefficient analysis showed significant positive and negative correlations among characteristics (e.g., fruit diameter and total soluble solids). Principal component analysis showed that fruit diameter, fruit weight, total soluble solids, total titratable acidity, fruit surface texture and adherence of albedo to pulp were the variables that most contributed to phenotypic variability. Genetic diversity analysis grouped accessions in four main clusters corresponding to traditional edible Chinese mandarins, Mediterranean mandarins, tangelos and tango hybrids and nonedible mandarins. A multiple factorial analysis showed that phenotypic diversity was associated with genetic diversity mainly for taste, shape and color traits. The results of this study will be used for the conservation of the indigenous germplasm, identification of varieties with valuable traits related to fruit quality and subsequent exploitation in citrus breeding programs.