Populations with diploid and triploid individuals co-occur in various plant and animal species, but detecting their relative frequencies is problematic. Microsatellite markers can be used to detect triploids that have three distinct alleles at a given locus, but cannot identify triploids that are partially or fully homozygous (i.e., possessing two or three copies of the same allele). Detection of partially homozygous triploids is sometimes possible with allozymes if no dosage compensation occurs. However, the inference of triploidy from uneven band intensities is not always reliable, making it difficult to estimate the actual proportion of triploids in a population. We present an iterative mathematical procedure for estimating the overall proportion of triploids from allozyme and microsatellite data. This method also estimates corrected allele frequencies by accounting for potentially hidden cases of homozygosity occurring in triploid individuals with multiple copies of an allele.