The expression of functional proteins in heterologous hosts is a core technique of modern biotechnology. The transfer to a suitable expression system is not always achieved easily because of several reasons: genes from different origins might contain codons that are rarely used in the desired host or even bear noncanonical codons, or the genes might hide expression-limiting regulatory elements within their coding sequence. These problems can also be observed when introducing foreign genes into genomes of microalgae as described in a growing number of detailed studies on transgene expression in these organisms. Particularly important for the use of algae as photosynthetic cell factories is a fundamental understanding of the influence of a foreign gene's codon composition on its expression efficiency. Therefore, the effect of codon usage of a chimeric protein on expression frequency and product accumulation in the green alga Chlamydomonas reinhardtii was analyzed. This fusion protein combines a constant region encoding the zeocin binding protein Ble with two different gene variants for the green fluorescent protein (GFP). It is shown that codon bias significantly affects the expression, but barely influences the final protein accumulation in this case.