Generation of new special rice varieties with particular inherited characteristics are one of the important targets in hybrid rice breeding. The selection and utilization of special rice germplasm resources derived from different regions and identification of their genotypes and analysis of their particular characteristics are of great significance for further promoting the genetic improvement. By using functional molecular markers InDel-E2, FMbadh2-E7, CAPSRa, CAPS-Ra, FMbadh2-E2, FMbadh2-E7A, FMbadh2-E7B, Ra-CAPS1 and Ra-CAPS2, the last 5 of which are newly designed in this study, combined with gene cloning and sequencing technology, we identified the fragrance genotypes of 32 high-quality fragrant rice materials and the black pericarp genotypes of 8 black rice varieties, respectively, from different regions. Of the 32 fragrant rice varieties, 28 were found to have the fragrance character derived from the known badh2 allele (badh2-E7), which was located on rice chromosome 8 and had an 8-bp deletion and three single nucleotide polymorphisms (SNPs) in exon 7, and which was non-functional for encoding betaine aldehyde dehydrogenase (BADH2), two varieties (Bancangxiangnuo and Baguixiang) were found to be heterozygotic with Badh2/badh2, and the other two (Xixiang and Lixiangzhan) were found to lack the mutation in the coding region of Badh2 including both exon 2 and exon 7, thus without their fragrance character being controlled by Badh2 alleles. In addition, we found that the black pericarp character of all 8 black rice varieties was controlled by the Ra/Pb gene on rice chromosome 4, which has a 2-bp (GT) deletion in exon 7. Moreover, we analyzed the genetic characteristics of Badh2 and Ra genes by developing a number of F2 populations, and found that the fragrance and black pericarp were controlled by a nuclear recessive gene and a nuclear dominant gene, respectively. In this study, the identification and genetic analysis of fragrance gene in 32 high-quality fragrant rice materials and black pericarp gene in 8 black rice varieties derived from the different regions have been made, which provides an important theoretical foundation for further breeding of fragrant hybrid rice and black hybrid rice with high quality and high yield by molecular marker-assisted selective breeding technology, as well as for improving the efficiency in breeding of special rice, and for making new breakthrough to the discovery of novel fragrance gene and black pericarp gene.