Human-infecting Cyclospora species have been a recognized cause of seasonal food-borne outbreaks of diarrheal illness in the United States and Canada since the 1990s. Prior to 2013, outbreak investigations were almost exclusively based on epidemiologic data because there were no laboratory methods to distinguish between outbreaks caused by distinct Cyclospora strains. Due to the challenges in obtaining sufficient parasite-derived material for research, the first draft genome was not published until 2015. To date, 36 samples have been genome sequenced; however, many of the published genomes suffer from low quality as they are fragmented (i.e., are not chromosome-level assemblies), were generated from pooled fecal specimens from multiple individuals, and contain contaminating sequences from other gastrointestinal microbes. The genome is estimated to be around 44 MBp large with a GC content of 52%. Initial efforts to develop a genotyping method to aid in outbreak investigations focused on organelle genomes, as they are small, present in high copy numbers, and are not subject to heterozygosity. However, both the mitochondrial and the apicoplast genomes are highly conserved and offer only limited genetic variability among isolates of human-infecting Cyclospora. Thus, nuclear markers should be included, and unique data analysis considerations are needed to account for the heterogeneity of nuclear loci. Multi-locus-sequence typing (MLST) is considered the most accessible strategy for routine Cyclospora genotyping. Since 2018, a targeted amplicon deep sequencing method based on eight markers has been in routine use at the Centers for Disease Control and Prevention. The resultant genotypes are used to compute a genetic distance via a heuristic algorithm that scores genetic relationships based on the number of shared haplotypes between genotypes and the frequency of these haplotypes in the study population. An analysis of 2841 genotypes obtained by this method revealed a population structure of two groups that seemed to be reproductively isolated and thus constitute distinct species (Cyclospora cayetanensis and Cyclospora ashfordi). The analysis also indicated that some genotypes recurred across multiple years. This pattern could be due to the environmental persistence of these genotypes within produce-growing regions. Alternatively, this could be an artifact from the limited discriminatory power of the method; parasites with high similarity in the eight markers may in fact be genetically distinct when expanding the analysis to additional markers. To this end, the Food and Drug Administration has recently developed an expanded panel consisting of 52 target loci. This method also includes a hybridization capture method to enrich for target DNA to increase sensitivity, which is advantageous for the genotyping of Cyclospora from environmental samples. Our understanding of the Cyclospora population structure and dynamics has dramatically increased after the introduction of routine genotyping since 2018. However, improved tools to investigate Cyclospora genomics are needed to refine our understanding of the temporal and geographical trends of Cyclospora in human transmission and in the environment.