In this study, we successfully identify shared morphological and molecular pathways between unrelated microphthalmia patients from different families, a bilateral microphthalmia patient who remained clinically unsolved following whole-genome sequencing and a unilateral microphthalmia patient with a PAX6 heterozygous missense variant (c.372C>A) p.(Asn124Lys). Here, PAX6 is linked to microphthalmia.