Broodstock management techniques in general, and gonadotropic treatments for vitellogenesis induction in particular, can influence the maternal provisioning of different compounds to the eggs, thus affecting embryo and larval competence. Among these, the abundance of certain transcripts as well as lipid content and fatty acid composition have been used as egg quality markers alongside other egg morphological parameters, such as egg size and the occurrence of abnormal cleavages during the first stages of embryonic development. Here, we evaluated the use of different markers of egg quality from farmed-raised European eel, Anguilla anguilla, broodstock reared on the same formulated diet but subjected to different pituitary extract administration schemes: weekly injections of salmon pituitary extract (SPE) in a constant dose or weekly injections of carp pituitary extract (CPE) at a stepwise increasing dose. Egg batches were categorized in two quality groups (high and low) according to their survival to the first feeding larval stage. In agreement with previous studies, unfertilized eggs and 4-h post fertilization embryos (16-cell stage) from SPE treated females had higher epcam expression levels than CPE ones, which is a molecule involved in cell-cell adhesion. When comparing treatments, batches from the SPE treatment had a lower incidence of cleavage abnormalities which could originate from compromised cell adhesion. On the other hand, this difference was not observed when comparing high-quality batches (i.e. those surviving up to the first-feeding stage) and low-quality ones. From the five genes analysed: epcam, dcbld1, plec, cenpf, and cenpk, only the latter had a differential expression between high- and low-quality groups both in unfertilized eggs and 4 h-post-fertilization embryos. This gene, cenpk, is involved in kinetochore assemblage during cell division and appears to be promising as egg quality marker in European eel in combination with epcam and dcbld1. Common biomarkers, such as egg size, total protein and lipid content, were similar between groups. However, although fatty acid composition was similar between quality groups, DHA and EPA content in unfertilized eggs was affected by the gonadotropic treatment applied to the female broodstock, and higher for the CPE treated females than the SPE ones. This entails that the hormonal treatments applied for vitellogenesis induction can influence the amount of specific fatty acids being transferred to the eggs, even for female broodstock that were fed the same high-quality diet.