I guess that you want to see the whole isolated DNA. Try to change the agarose percent first. When you performed the PCR, you amplified an specific part of the DNA so is small compared with the whole isolated DNA. Try to use a low % of agarose gel. Good Luck!

Yes, I agree with Lenin. Most likely, your genomic DNA is probably too large to migrate into the gel. When you say you can see genomic DNA of other taxa, to which are you referring?

to visualize your isolated genomic dna, you need to prepare at least 0.8% agarose gel and put appropriate amount of gelRed (e.g 0.5 ul of gelred for 0.8% agarose in 25 ml 1X tae buffer). Run at 75 V for 30 min. GelRed can be put in agarose-tae mixed solution before heating in a microwave oven because gelred is thermostable.

You can also check the concentration and purity of isolated genomic dna. The troubleshooting can be done if you recognize which problem that turn to the negative result after viewing your gel. It may be caused by the isolation technique either using conventional method or commercial kit.

OR, It may be something in whipworm that affects the result of getting a good isolated genomic dna. You have to check and identify the problem by comparing it with other taxons based on the rare characteristics.

Thank you all for advise. I usually work with fish samples and this have never happen to me. I will try to decrease gel concentration.

Out of curiosity, what size range can you resolve for your genomic DNA from the fish samples?