Fertilisation rates vary considerably between spawning events, from 0% to 100%. Individual spawning trials in these studies typically resulted in an average fertilisation rate per group of females (sample sizes of 25 to 100 females per trial) of 50% to 85%. Some individuals produce eggs well below, and above, this average. Biologically, poor fertilisation can be due to poor quality eggs, poor sperm quality, low sperm count per spermatophore or broodstock in a stressed condition. Physical dimensions of the spawning tank can also have an effect. Disruption of normal behaviour during the spawning event itself, such as the female colliding with the side of small tanks, may result in suboptimal mixing of sperm and eggs, resulting in low fertilisation rates.

Fertilisation can be determined by other methods beside's microscopic observation. Although high tech and requiring expensive equipment, flow cytometry is one method that lends itself to automation and would potentially be a useful method for the purpose of monitoring large commercial operations when problems arose. However, flow cytometry requires specialised equipment and samples would have to be analysed off-site at a research laboratory rather than the hatchery. Nevertheless, flow cytometry was investigated as a possible method to determine fertility since a larger number of samples can be analyzed quickly. The technique relies on incubating a sub-sample of eggs in the presence of a special nucleus deoxyribonucleic acid (DNA) fluorescence dye. The intensity of the fluorescence is proportion to the amount of DNA. An unfertilised haploid egg has half the amount of DNA as a fertilised diploid egg (zygote). A subsample of several hundred to thousands of eggs from a spawning can be pumped through a flow cytometer and the relative proportion of unfertilised and fertilised eggs therefore determined. The technique, however, depends partially on the size and shape of the fluorescing object. Our research found that the nuclei of prawn eggs are highly irregular in size and shape (Fig. 3.1). Because of this it was impossible to distinguish between haploid and diploid eggs by this method.

Eggs may be added to a Bogorov tray (a plastic tray with routed lanes used for counting plankton). However, any clear bottom container, such as a glass petri dish will suffice. One to two hundred eggs should be scored to obtain an accurate reflection of fertility rate. Use a microscope with illumination from below the sample. It is best to first make a total count of eggs in the container under low magnification. Afterwards, using a higher magnification, count the number of eggs that have a symmetrical cleavage pattern.