Information on complete human mitochondrial DNA has revealed polymorphisms located in the coding region, which are useful for a more secure mtDNA haplogroup subdivision. We sequenced 1580 bp in the coding region informative for subclassification of haplogroup H, the most poorly resolved European haplogroup when studying only control-region variation. This revealed nine coding polymorphisms (at positions 3010, 3915, 3992, 4024, 4336, 4745, 4769, 4793 and 6776, besides the diagnostic position 7028) that allowed subclassification of around 80% of the 306 Iberian H samples in eight subhaplogroups. Frequencies for these haplogroups vary widely, with half of the samples sharing the substitution at position 3010 (but some structure is already apparent within this subhaplogroup). The HVRI diversity suggested the following age estimates for some subhaplogroups: 3010: 13,400±3000 years; 6776: 8600±2800 years; 4336: 4700±2700 years; 3915: 17,300±9100 years. Those ages indicate that these H subhaplogroups may be informative for different time scales of European demographic history.