With the objective to identify deleterious recessive mutations, we have scanned the genome of 5,271 French Manech Tête Rousse (MTR) dairy sheep using 50k SNP phased genotypes and pedigree data. Five deficient homozygous haplotypes, named MTRDHH1 to MTRDHH5, were identified. These haplotypes showed a highly significant deficit of homozygous animals ranging from 84 to 100%, and a carrier frequency ranging from 7.8 to 16.6%. By comparing at-risk matings (between carriers) and safe matings, some of these haplotypes were associated with a reduced success of artificial insemination (MTRDHH2), and/or an increased stillbirth rate (MTRDHH1 and 2) suggesting the segregation of recessive variants leading to embryo and/or perinatal lethality affecting fertility. Other haplotypes are likely to be associated with lamb morphological disorders or counter-selection based on breed standard. For each haplotype, the most probable candidate genes were highlighted based on their roles in lethal phenotypes, genetic disorders, hornless or coat color.