Understanding the skeletal development and deformations for aquaculture candidate fish species is vital for successful aquaculture practices. Developmental abnormalities at early life stages may reduce fish viability, growth, and wellbeing. This study was carried out to investigate the skeletal ontogeny and skeletal deformities of the European flounder (Platichthys flesus) at early life stage. Artificially produced European flounder larvae (n = 270) were randomly selected at a regular interval (30 fish at each sampling) from hatching to 50 days post-hatch (dph) and their skeletal ontogeny and skeletal deformations were evaluated by using bone and cartilage staining techniques. The average length of fish was 2.71 ± 0.04 mm at 0 dph and reached 19.76 ± 1.7 mm at 50 dph. The notochord began to form at 10 dph and finished flexion at 30 dph. Hypural rays appeared between 10 and 15 dph, followed by appearance of tail fin rays. Urostyle developed at 30 dph and began to ossify at 40 dph. Meristic characters showed an interspecific variation. At least one type of deformation was observed on 23.3% of larvae, and a total of 13 different deformations were identified. The most common deformation was the deformed vertebra which was observed 13 times followed by deformed dorsal fin ray, deformed caudal fin ray, and deformed neural arch and/or spine. Skeletal development during the early life stage of European flounder under culture conditions could be useful for future culture attempts and for early detection of skeletal deformations.