SSRs have long been considered as almost ideal markers for genetic diversity analysis. With the increasing availability of sequencing data, SNPs and InDels become major classes of codominant markers with genome wide coverage. We have analyzed the respective values of SSRs, InDels, and SNPs for intra and interspecific Citrus genetic diversity analysis. Moreover, we have compared the diversity structure revealed by markers mined in a single heterozygous genotype (the clementine) and markers mined in a large interspecific survey. A random set of 25 markers was selected for each marker class to genotype 48 citrus accessions. SSRs were the most polymorphic markers at the intraspecific level allowing complete varietal differentiation within basic taxa (Citrus reticulata, Citrus maxima, Citrus medica). However, SSRs gave the lowest values for interspecific differentiation, followed by SNPs and InDels, that displayed low intraspecific variability but high interspecific differentiation. A clear effect of the discovery panel was observed for SNPs and InDels. The ascertainment biases associated with the clementine heterozygosity mining resulted mainly in an over estimation of within C. reticulata diversity and an underestimation of the interspecific differentiation. Therefore SSRs are very useful for intraspecific structure analysis while SNPs and InDels mined in large discovery panel will be more powerful to decipher the interspecific mosaic structure of secondary cultivated species.