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Can you describe the spots? What is their size?
Are they raised or flat, smooth etc?
Any itch or penile discharge?
How long have they been a problem?
How many do you have?
The skin over the penis is just like skin elsewhere in that it can get normal bumps which are not STD related. Liver spots are not a problem, merely increased pigmentation. However if the large one has changed significantly in size or texture then it is worth having it rechecked.
Often with skin lesions, I recommend taking a digital photo with the date and then checking after a period of time to see the extent of changes. Any doubt though, do see a dermatologist. He/she may suggest taking a biopsy to look at the nature of the skin and whether there is reason to remove the lesion.
Not all skin lesions will have a relationship to sun exposure. A frequently missed place for a type of melanoma is actually the sole of the foot.
I suspect that this is just a liver spot and changes to these are normal with age, however anything that changes signficantly needs to be followed up. A very large brown patch may be erythrasma which is treated with antibiotics although this is more groin than penile related.