The difference in plain language
Margin compares profit to the sale price. Markup compares profit to the cost. Because they use different denominators, they will not match unless profit is zero. This is why a seller can say "I use a 100 percent markup" and still only have a 50 percent gross margin before fees and shipping.
For marketplace sellers, gross margin is only the first layer. It ignores marketplace fees, payment processing, shipping, packaging, returns, and ads. Use this page to understand the relationship between cost and price, then use the main profit calculator to include the full selling cost.