Concentrated urine. Although classic urine color is a yellow amber, the color reflects the items the body has discarded thru the kidneys. Usually, darker urine means the baby has less fluid to discard at that moment so it is more concentrated. Certain foods, treats, or medicines may tint the urine. The diaper stain may look a little funny for a variety of reasons. Check with your doctor for specific concerns.
Fluids. Dark urine may mean not enough fluids. If over two months of age consider giving small amounts of water between feeds. If there is an unusual odor seek an opinion from your MD. If newborn and breastfeeding, increase the time at each breast and ask mom to drink plenty of water. If formula fed infant, be sure you are mixing the powder to water ratio correctly.
Jaundiced/dehydrated. If he is a newborn and jaundiced, the yellow color may be him getting rid of the extra bilirubin (yellow) in his blood. Otherwise, he may be a bit dehydrated until your milk comes in. This is normal for the first couple of days. If he has been sick or vomitting, dark yellow urine can be a sign of dehydration and he should be seen by his physician.