In recent years, certain cyanobacteria are reported to lack functional PS II of photosynthesis. These unicellular Nitrogen-fixing cyanobacteria termed as UCYN-A are yet not cultured in laboratory and are major contributor to the nitrogen input of marine ecosystem. Genome sequence of one such cyanobacterium is available, for which codon selection pattern is analysed using various in-silico and statistical techniques. It is identified that T and/or A ending codons were predominant. Compositional mutational bias was observed to be one of the major factors responsible for codon bias among the genes. A strong positive correlation between effective number of codons (Nc) and GC3S content was also observed showing that the codon usage was affected by gene nucleotide composition. Translational selection and gene length were observed to have a minor role in influencing the codon usage variation among the genes. Multivariate statistical analysis identified that there is not any major explanatory axis in this organism. A set of 16 codons were determined as the ‘optimal codons’ using χ 2 test (P < 0.01). Thus, above analysis reveals that compositional constraints plays major role in selecting codons in UCYN-A genome which is also affected by translational selection, although in low amount.