She is pregnant and she did not pray for nine months, then she repented. What is the ruling on her marriage?

The scholars (may Allah have mercy on them) differed as to whether the one who does not pray is a kaafir, if he does not deny that it is obligatory. Some of them – and this is the view of Imam Ahmad and a number of the early generations – said that he is a kaafir in the sense of kufr that puts one beyond the pale of Islam, and he is to be regarded as an apostate. 

The majority of scholars said that he does not become a kaafir by not praying, so long as he does not deny that it is obligatory, but he should be asked to repent for three days; if he repents, all well and good, but if he does not, he is to be executed as a hadd punishment, not on the grounds that he has become a kaafir.

The more correct view is the former, which is that the one who does not pray is a kaafir. This is the view reflected in fatwas given on this website. 

See also the answer to question no. 5208 

Secondly: 

If a person prays sometimes and not at other times, there is a difference of opinion among those who say that he is a kaafir in this case. Some of them say that he becomes a kaafir if he omits one obligatory prayer deliberately until the time for it is over. Others say that he does not become a kaafir unless he stops praying altogether. The latter is the view favored by Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him). For more information, please see the answer to question no. 83165 . 

Thirdly: 

If you were praying before marriage, then the marriage contract is valid, and there is no problem with it. 

If it so happened that you stopped praying altogether after marriage, for a period of nine months as you mentioned, then this is subject to the difference of scholarly opinion mentioned above concerning the ruling on one who does not pray. The opinion of the majority of scholars is that the one who does not pray is not deemed to be an apostate, so there is no problem, and the marriage remains valid, especially since you repented after that and adhered to praying regularly.

 But according to the view of those who think that the one who does not pray becomes a kaafir and apostate, the marriage is not completely annulled because of that; rather the matter is to be left till the end of the ‘iddah. If the partner who became an apostate repents before the end of the ‘iddah, then the marriage remains as it was. But if the ‘iddah ends (without that partner having repented), then they are to be separated and the marriage is annulled. 

Rather, Shaykh al-Islam [Ibn Taymiyah] thinks that even after the end of the ‘iddah there is still an opportunity for the partners to go back to their previous marriage contract, if the one who became an apostate repents before the woman remarries. 

Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) said: If both or one of them becomes a kaafir after consummation of the marriage, the matter is to be left until the end of the ‘iddah and the marriage is not to be annulled yet. Rather we should wait until the ‘iddah ends. Then if they come back to Islam, the marriage remains valid. It says in ar-Rawd: If the one who became an apostate repents before (the ‘iddah) ends, then their marriage remains valid, otherwise the marriage is to be annulled from the time he apostatised. 

Shaykh al-Islam [Ibn Taymiyah] has the same opinion concerning this issue as is mentioned above about the first issue. He says: Before the end of the ‘iddah, the woman is not allowed to marry someone else; after the end of the ‘iddah she may marry someone else. But if she does not want to get married, in the hope that her husband may come back to Islam, then she is allowed that option. 

End quote from ash-Sharh al-Mumti‘, 12/249. See also: al-Mawsoo‘ah al-Fiqhiyyah, 7/35 

To sum up: 

So long as you have repented and adhered to regular prayer, and you are still pregnant and have not yet given birth, then your marriage is valid and there is no problem with it, in sha Allah. 

But what really matters here is that you learn a lesson from this, which is that prayer is too important to be ignored because of laziness or one’s own whims and desires. It is the most important physical act and is the most important thing that Allah demands of His slaves after their entering His religion. 

And Allah knows best.