A method of determining inheritance of maternal haplotypes in two fetuses of a female fertilized by a male using a maternal biological sample, the method comprising: identifying a first group of a plurality of first loci on a first chromosome, wherein the female is heterozygous for a respective first allele and a respective second allele at each first locus, a first maternal haplotype having the first alleles and a second maternal haplotype having the second alleles; determining that the two fetuses inherit the respective first alleles at the first loci from the male; identifying a second group of a plurality of second loci on the first chromosome, wherein the first maternal haplotype has a respective third allele and the second maternal haplotype has a respective fourth allele at each second locus of the second group, and determining that the two fetuses inherit the respective fourth alleles at the second loci from the male; measuring a first amount of the respective first alleles and a second amount of the respective second alleles that are present at the first loci in DNA fragments of a biological sample from the female, the biological sample including cell-free DNA of the female and the two fetuses; measuring a third amount of the respective third alleles and a fourth amount of the respective fourth alleles that are present at the second loci in DNA fragment of the biological sample; and determining inheritance of maternal haplotypes in the two fetuses by: (i) identifying both fetuses as having inherited the first maternal haplotype when the first amount is statistically higher than the second amount and the third amount is statistically equal to the fourth amount, (ii) identifying both fetuses as having inherited the second maternal haplotype when the first amount is statistically equal to the second amount and the fourth amount is statistically higher than the third amount, or (iii) identifying one of the fetuses as inheriting the first maternal haplotype and the other fetus as inheriting the second maternal haplotype when the first amount is statistically higher than the second amount and when the fourth amount is statistically higher than the third amount. identifying a first group of a plurality of first loci on a first chromosome, wherein the female is heterozygous for a respective first allele and a respective second allele at each first locus, a first maternal haplotype having the first alleles and a second maternal haplotype having the second alleles; determining that the two fetuses inherit the respective first alleles at the first loci from the male; identifying a second group of a plurality of second loci on the first chromosome, wherein the first maternal haplotype has a respective third allele and the second maternal haplotype has a respective fourth allele at each second locus of the second group, and determining that the two fetuses inherit the respective fourth alleles at the second loci from the male; measuring a first amount of the respective first alleles and a second amount of the respective second alleles that are present at the first loci in DNA fragments of a biological sample from the female, the biological sample including cell-free DNA of the female and the two fetuses; measuring a third amount of the respective third alleles and a fourth amount of the respective fourth alleles that are present at the second loci in DNA fragment of the biological sample; and determining inheritance of maternal haplotypes in the two fetuses by: (i) identifying both fetuses as having inherited the first maternal haplotype when the first amount is statistically higher than the second amount and the third amount is statistically equal to the fourth amount, (ii) identifying both fetuses as having inherited the second maternal haplotype when the first amount is statistically equal to the second amount and the fourth amount is statistically higher than the third amount, or (iii) identifying one of the fetuses as inheriting the first maternal haplotype and the other fetus as inheriting the second maternal haplotype when the first amount is statistically higher than the second amount and when the fourth amount is statistically higher than the third amount. (i) identifying both fetuses as having inherited the first maternal haplotype when the first amount is statistically higher than the second amount and the third amount is statistically equal to the fourth amount, (ii) identifying both fetuses as having inherited the second maternal haplotype when the first amount is statistically equal to the second amount and the fourth amount is statistically higher than the third amount, or (iii) identifying one of the fetuses as inheriting the first maternal haplotype and the other fetus as inheriting the second maternal haplotype when the first amount is statistically higher than the second amount and when the fourth amount is statistically higher than the third amount.