After her meetings in the Red Sea city of Jiddah, she told German journalists travelling with her that she raised human rights concerns with Saudi leaders, including the rights of women.
She said Saudi Arabia's war in Yemen also was discussed. For more than two years, the kingdom has been bombing Yemeni rebels aligned with Saudi Arabia's regional Shiite rival, Iran.
The conflict there has driven the Arab world's poorest countries to the brink of famine, with 27 million people needing humanitarian or protection assistance.
Saudi Arabia and Iran also back opposite sides of the conflict in Syria, and Germany was one of six international powers that negotiated the nuclear deal with Iran to which Saudi Arabia objected.
As is customary, Saudi officials did not comment on the details of the meetings.
After her meeting with the Saudi king, Merkel held talks with Crown Prince Mohammed bin Nayef, who oversees security forces and counterterrorism, and Deputy Crown Prince Mohammed bin Salman, who has a vast portfolio overseeing defence and the economy.
She also raised the case of Raif Badawi, a Saudi blogger whose public lashing drew international condemnation from even the kingdom's closest Western allies. He is serving a 10-year prison sentence for blog posts critical of the country's powerful religious establishment.
Having scheduled a meeting with Saudi businesswomen during her two-day visit, Merkel acknowledged there have been "significant changes in the role of women" since her last visit in 2010. She cited the historic first-time participation of women in Saudi Arabia's only elections for local council seats in 2015.
"I have the impression that the country is in a phase of change and that a lot more is possible now than some years ago, but it's still a long way away from having achieved what we would understand as equality," Merkel said.
Like other high-profile female visitors, Merkel did not cover her hair or wear a traditional flowing black robe upon arrival in the kingdom.
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