A multilocus genotype is the combination of alleles found at two or more loci in a single individual.
For example, in a diploid species, if there are two SNP loci and the first locus has alleles A and G, while the second locus has alleles T and C, the multilocus genotype can be represented as . If the genome is not haploid then the multilocus genotype does not necessarily determine which alleles co-occur on chromosomes. In the example, if the two loci are located on the same chromosome the possibilities are either or . Where A-T represents a haplotype with alleles A and T together on one chromosome and G and C together on the other. If the haplotypes are determined the multilocus genotype is referred to as a phased genotype, otherwise it is referred to as unphased. Some authors[1] [2] suggest that the term multilocus genotype should only be applied to phased multilocus data while others[3] apply it to unphased multilocus data as well. The combination of alleles at two or more loci on a single chromosome make up a haplotype and the two haplotypes in a diploid individual make up the diplotype (a synonym for a phased multilocus genotype).