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The cyprinid genus Ballerus includes two species differing in skeletal characters (lateral line scale and gill raker counts) and feeding habits. The white-eye bream B. sapa is benthivorous and has lower numbers of lateral line scales and gill rakers than its sister species, the blue bream B. ballerus, which is planktivorous. The former species exhibits several times higher triiodothyronine (T3) level in serum compared to the latter. Thyroid hormones (THs) control development of skeletal and non-skeletal structures in fish, thus the observed difference in T3 level might contribute to morphological divergence of the two Ballerus species. We report the phenotypic and transcriptomic effects of experimental increase of thyroid level in B. ballerus during its early development. The numbers of scales and gill rakers appeared to be significantly decreased in TH-treated fish, approaching the limits of these characters in B. sapa. Illumina RNA-seq analysis demonstrated high number of differentially expressed genes between control and TH-treated B. ballerus in brain and liver (1212 genes at FDR < 2 %). Most of these genes encode proteins involved in energetic metabolism, transcription factors or binding proteins, and some morphogens. Many homeobox genes (up to 14) were also under effect of THs. We also detected 44 genes involved in lateral line development and 53 genes involved in gill arch and gill raker patterning. Some of detected genes are responsible for cell cycle and organ size (Hippo signaling pathway) being very promising for search of hormonal bases of developmental heterochronies. Our experiment shows that the divergence in pattern of TH secretion could result in evolutionary transformation of morphological characters involved in resource partitioning because the increased gill raker number in naturally TH-deficient B. ballerus is apparent adaptation to its planktivorous mode of feeding.